6-31464003-T-G

Variant names:

• chr6-31464003-T-G
• rs2395029
• ENST00000541196.3:n.198-50T>G

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_Strong BS1_Supporting BS2

The ENST00000414046.3(HCP5):​n.743T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0287 in 512,480 control chromosomes in the GnomAD database, including 368 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.025 (63 hom., cov: 32)
  • Exomes 𝑓: 0.030 (305 hom.)
• Consequence: HCP5 ENST00000414046.3 non_coding_transcript_exon
• Clinical Significance: Conflicting classifications of pathogenicity no assertion criteria provided P:1 B:1
• Conservation: PhyloP100: 0.180

Genes affected

HCP5 (HGNC:21659): (HLA complex P5)

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0247 (3749/152004) while in subpopulation SAS AF= 0.0484 (233/4810). AF 95% confidence interval is 0.0433. There are 63 homozygotes in gnomad4. There are 1788 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
• BS2: High Homozygotes in GnomAd4 at 63 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCP5	NR_040662.1	n.733T>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCP5	ENST00000541196.3	n.198-50T>G		intron_variant	Intron 2 of 3	1
HCP5	ENST00000414046.3	n.743T>G		non_coding_transcript_exon_variant	Exon 2 of 2	4
HCP5	ENST00000670109.1	n.706T>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0247 AC: 3750 AN: 151886 Hom.: 64 Cov.: 32

Gnomad AFR AF: 0.00761

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.0139

Gnomad ASJ AF: 0.0428

Gnomad EAS AF: 0.00851

Gnomad SAS AF: 0.0492

Gnomad FIN AF: 0.00932

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0367

Gnomad OTH AF: 0.0254

GnomAD3 exomes AF: 0.0270 AC: 6123 AN: 226874 Hom.: 161 AF XY: 0.0292 AC XY: 3603 AN XY: 123380

Gnomad AFR exome AF: 0.00788

Gnomad AMR exome AF: 0.00953

Gnomad ASJ exome AF: 0.0446

Gnomad EAS exome AF: 0.00314

Gnomad SAS exome AF: 0.0520

Gnomad FIN exome AF: 0.00946

Gnomad NFE exome AF: 0.0339

Gnomad OTH exome AF: 0.0284

GnomAD4 exome AF: 0.0304 AC: 10943 AN: 360476 Hom.: 305 Cov.: 0 AF XY: 0.0323 AC XY: 6673 AN XY: 206568

Gnomad4 AFR exome AF: 0.00989

Gnomad4 AMR exome AF: 0.00951

Gnomad4 ASJ exome AF: 0.0431

Gnomad4 EAS exome AF: 0.00245

Gnomad4 SAS exome AF: 0.0469

Gnomad4 FIN exome AF: 0.0107

Gnomad4 NFE exome AF: 0.0338

Gnomad4 OTH exome AF: 0.0319

GnomAD4 genome AF: 0.0247 AC: 3749 AN: 152004 Hom.: 63 Cov.: 32 AF XY: 0.0241 AC XY: 1788 AN XY: 74312

Gnomad4 AFR AF: 0.00766

Gnomad4 AMR AF: 0.0139

Gnomad4 ASJ AF: 0.0428

Gnomad4 EAS AF: 0.00853

Gnomad4 SAS AF: 0.0484

Gnomad4 FIN AF: 0.00932

Gnomad4 NFE AF: 0.0367

Gnomad4 OTH AF: 0.0251

Alfa AF: 0.0337 Hom.: 202

Bravo AF: 0.0239

Asia WGS AF: 0.0220 AC: 76 AN: 3476

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

Autism spectrum disorder Pathogenic:1

Likely risk allele, no assertion criteria provided

clinical testing

Gene Friend Way, National Innovation Center

Jul 28, 2023

A mutation in HLA complex P5. Many recent studies have shown that HCP5 SNP sequences are strongly associated with various chronic and infectious diseases. Several alleles of HLA genes has been reported to be associated with autism, intellectual disability, schizophrenia (PMID: 30976114). rs2395029 is in complete linkage disequilibrium with HLA-B*5701 (PMID: 31421661), which is a risk allele of intellectual disability (PMID: 30976114). -

Abacavir hypersensitivity Benign:1

Benign, no assertion criteria provided

literature only

OMIM

Mar 07, 2025

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.7
DANN	Benign	0.20

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2395029; hg19: chr6-31431780;