6-31466334-A-G

Variant names:

• chr6-31466334-A-G
• rs3094604
• ENST00000414046.3:n.3074A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000414046.3(HCP5):​n.3074A>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 0.143 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 ENST00000414046.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 31 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCP5	ENST00000414046.3	n.3074A>G		non_coding_transcript_exon_variant	Exon 2 of 2	4
HCP5	ENST00000467369.2	n.217+2826A>G		intron_variant	Intron 2 of 2	4
HCP5	ENST00000666495.2	n.95+3055A>G		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.110 AC: 4561 AN: 41354

American (AMR) AF: 0.101 AC: 1543 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3470

East Asian (EAS) AF: 0.158 AC: 817 AN: 5176

South Asian (SAS) AF: 0.209 AC: 1007 AN: 4822

European-Finnish (FIN) AF: 0.124 AC: 1319 AN: 10606

Middle Eastern (MID) AF: 0.203 AC: 59 AN: 290

European-Non Finnish (NFE) AF: 0.171 AC: 11594 AN: 67988

Other (OTH) AF: 0.135 AC: 285 AN: 2106

Alfa AF: 0.153 Hom.: 4772

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
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs3094604; hg19: chr6-31434111;