rs3094604

chr6-31466334-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000666495.2(HCP5):n.95+3055A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 151,960 control chromosomes in the GnomAD database, including 1,795 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.14 (1795 hom., cov: 32)
• Consequence: HCP5 ENST00000666495.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCP5	ENST00000666495.2	n.95+3055A>G		intron_variant, non_coding_transcript_variant
HCP5	ENST00000414046.3	n.3074A>G		non_coding_transcript_exon_variant	2/2	4
HCP5	ENST00000467369.2	n.217+2826A>G		intron_variant, non_coding_transcript_variant		4
HCP5	ENST00000674016.1	n.97+2204A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21674 AN: 151840 Hom.: 1793 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.202

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.135

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.143 AC: 21684 AN: 151960 Hom.: 1795 Cov.: 32 AF XY: 0.142 AC XY: 10527 AN XY: 74286

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.135

Alfa AF: 0.157 Hom.: 967

Bravo AF: 0.136

Asia WGS AF: 0.193 AC: 668 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	6.6
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3094604; hg19: chr6-31434111;