rs3131643

Variant names:

• chr6-31475005-G-A
• rs3131643
• ENST00000467369.2:n.218-2022G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-31475005-G-A
• chr6-31475005-G-C
• chr6-31475005-G-T

Variant summary

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

The ENST00000467369.2(HCP5):​n.218-2022G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 151,818 control chromosomes in the GnomAD database, including 1,343 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 0.12 (1343 hom., cov: 32)
• Consequence: HCP5 ENST00000467369.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.141 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	ENST00000467369.2	n.218-2022G>A		intron_variant	Intron 2 of 2	4
HCP5	ENST00000666495.2	n.96-2022G>A		intron_variant	Intron 1 of 1
HCP5	ENST00000674016.2	n.889-2022G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18492 AN: 151700 Hom.: 1340 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.0728

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0685

Gnomad SAS AF: 0.0436

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.122 AC: 18505 AN: 151818 Hom.: 1343 Cov.: 32 AF XY: 0.117 AC XY: 8710 AN XY: 74238

African (AFR) AF: 0.122 AC: 5043 AN: 41324

American (AMR) AF: 0.0727 AC: 1105 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 475 AN: 3464

East Asian (EAS) AF: 0.0686 AC: 354 AN: 5158

South Asian (SAS) AF: 0.0441 AC: 212 AN: 4810

European-Finnish (FIN) AF: 0.113 AC: 1192 AN: 10572

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9717 AN: 67976

Other (OTH) AF: 0.103 AC: 216 AN: 2100

Alfa AF: 0.140 Hom.: 4885

Bravo AF: 0.122

Asia WGS AF: 0.0840 AC: 292 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.1
DANN	Benign	0.83
PhyloP100		-0.21
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: rs3131643; hg19: chr6-31442782;