6-31466334-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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 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
HCP5	ENST00000674016.1	n.97+2204A>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

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;