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Merged
Peter-J-Freeman merged 2 commits into from
Jun 24, 2026
Merged

Develop #845

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9c292f6
Ensure chrY is only pushed to AlTs in PAR regions when chrX is present
Peter-J-Freeman Jun 24, 2026
66a8967
Merge pull request #844 from openvar/par_regions
Peter-J-Freeman Jun 24, 2026
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3 changes: 3 additions & 0 deletions VariantValidator/modules/vvMixinCore.py
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Original file line number Diff line number Diff line change
Expand Up @@ -923,6 +923,9 @@ def validate(self,
chrY = True
if chrX is True and chrY is True:
par = True
variant.warnings.append('ParRegionWarning: Variant is located in a pseudoautosomal region (PAR) of '
'the X and Y chromosomes, so the Y context description has been moved to '
'alt_genomic_loci')

for alt_gen_var in multi_gen_vars:
if 'NC_' in alt_gen_var.ac:
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90 changes: 88 additions & 2 deletions tests/test_liftover.py
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Original file line number Diff line number Diff line change
@@ -1,20 +1,106 @@
from VariantFormatter import simpleVariantFormatter
import VariantValidator
vval = VariantValidator.Validator()

from unittest import TestCase


class TestLiftover(TestCase):

def test_gene_variant(self):
def test_gene_variant_par_vf(self):
result = simpleVariantFormatter.format('NC_000023.10:g.591732del', 'GRCh37', 'refseq', "raw", False, True)
assert result["NC_000023.10:g.591732del"]["NC_000023.10:g.591732del"]["g_hgvs"] == "NC_000023.10:g.591732del"
assert result["NC_000023.10:g.591732del"]["NC_000023.10:g.591732del"]["p_vcf"] == "X:591731:TA:T"
assert result["NC_000023.10:g.591732del"]["NC_000023.10:g.591732del"]["hgvs_t_and_p"]["NM_000451.3"]["alt_genomic_loci"][0]["grch37"]["hgvs_genomic_description"] == "NC_000024.9:g.541732del"
assert result["NC_000023.10:g.591732del"]["NC_000023.10:g.591732del"]["genomic_variant_warnings"] == "ParRegionWarning: Variant is located in a pseudoautosomal region (PAR) of the X and Y chromosomes, so the Y context description has been moved to alt_genomic_loci"

result = simpleVariantFormatter.format('NC_000024.9:g.541732del', 'GRCh37', 'refseq', "raw", False, True)
assert result["NC_000024.9:g.541732del"]["NC_000024.9:g.541732del"]["g_hgvs"] == "NC_000024.9:g.541732del"
assert result["NC_000024.9:g.541732del"]["NC_000024.9:g.541732del"]["hgvs_t_and_p"]["NM_000451.3"]["alt_genomic_loci"][0]["grch37"]["hgvs_genomic_description"] == "NC_000024.9:g.541732del"
assert result["NC_000024.9:g.541732del"]["NC_000024.9:g.541732del"]["genomic_variant_warnings"] == "ParRegionWarning: Variant is located in a pseudoautosomal region (PAR) of the X and Y chromosomes, so the Y context description has been moved to alt_genomic_loci"


def test_gene_variant_par_vf_non_par(self):
result = simpleVariantFormatter.format('NC_000024.9:g.9197998C>T', 'GRCh37', 'refseq', 'mane_select', False, 'False')
assert result["NC_000024.9:g.9197998C>T"]["NC_000024.9:g.9197998C>T"]["g_hgvs"] == "NC_000024.9:g.9197998C>T"

def test_mito_variant(self):
def test_mito_variant_vf(self):
result = simpleVariantFormatter.format('NC_012920.1:g.100del', 'GRCh37', 'refseq', None, False, True)
assert result["NC_012920.1:g.100del"]["NC_012920.1:g.100del"]["g_hgvs"] == "NC_012920.1:m.101del"
assert result["NC_012920.1:g.100del"]["NC_012920.1:g.100del"]["p_vcf"] == "M:99:TG:T"

def test_gene_variant_par_vv(self):
variant = 'NC_000023.10:g.591732del'
genome_build = 'GRCh38'
select_transcripts = 'all'
result = vval.validate(variant, genome_build, select_transcripts, transcript_set="refseq").format_as_dict(test=True)
assert result["NM_000451.4:c.100del"]["primary_assembly_loci"]["grch38"]["hgvs_genomic_description"] == "NC_000023.11:g.630997del"
assert result["NM_000451.4:c.100del"]["primary_assembly_loci"]["grch37"]["hgvs_genomic_description"] == "NC_000023.10:g.591732del"
assert {
"grch38": {
"hgvs_genomic_description": "NC_000024.10:g.630997del",
"vcf": {
"alt": "T",
"chr": "Y",
"pos": "630996",
"ref": "TA"
}
}
} in result["NM_000451.4:c.100del"]["alt_genomic_loci"]
assert {
"grch37": {
"hgvs_genomic_description": "NC_000024.9:g.541732del",
"vcf": {
"alt": "T",
"chr": "Y",
"pos": "541731",
"ref": "TA"
}
}
} in result["NM_000451.4:c.100del"]["alt_genomic_loci"]
assert ("ParRegionWarning: Variant is located in a pseudoautosomal region (PAR) of the X and Y chromosomes, "
"so the Y context description has been moved to alt_genomic_loci") in result[
"NM_000451.4:c.100del"]["validation_warnings"]

variant = 'NC_000024.10:g.630997del'
genome_build = 'GRCh38'
select_transcripts = 'all'
result = vval.validate(variant, genome_build, select_transcripts, transcript_set="refseq").format_as_dict(test=True)
assert result["NM_000451.4:c.100del"]["primary_assembly_loci"]["grch38"]["hgvs_genomic_description"] == "NC_000023.11:g.630997del"
assert result["NM_000451.4:c.100del"]["primary_assembly_loci"]["grch37"]["hgvs_genomic_description"] == "NC_000023.10:g.591732del"
assert {
"grch38": {
"hgvs_genomic_description": "NC_000024.10:g.630997del",
"vcf": {
"alt": "T",
"chr": "Y",
"pos": "630996",
"ref": "TA"
}
}
} in result["NM_000451.4:c.100del"]["alt_genomic_loci"]
assert {
"grch37": {
"hgvs_genomic_description": "NC_000024.9:g.541732del",
"vcf": {
"alt": "T",
"chr": "Y",
"pos": "541731",
"ref": "TA"
}
}
} in result["NM_000451.4:c.100del"]["alt_genomic_loci"]
assert ("ParRegionWarning: Variant is located in a pseudoautosomal region (PAR) of the X and Y chromosomes, "
"so the Y context description has been moved to alt_genomic_loci") in result[
"NM_000451.4:c.100del"]["validation_warnings"]

def test_gene_variant_non_par_vv(self):
variant = 'NC_000024.9:g.9197998C>T'
genome_build = 'GRCh37'
select_transcripts = 'all'
result = vval.validate(variant, genome_build, select_transcripts, transcript_set="refseq").format_as_dict(test=True)
assert result["NM_001243721.2:c.911C>T"]["primary_assembly_loci"]["grch37"]["hgvs_genomic_description"] == "NC_000024.9:g.9197998C>T"


# <LICENSE>
# Copyright (C) 2016-2026 VariantValidator Contributors
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