rs2248462

Variant names:

• chr6-31479019-G-A
• rs2248462
• ENST00000718213.1:n.96-11643G>A

Variant summary

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

The ENST00000718213.1(HCP5):​n.96-11643G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 151,792 control chromosomes in the GnomAD database, including 3,184 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 0.19 (3184 hom., cov: 32)
• Consequence: HCP5 ENST00000718213.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133
• Publications: 65 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718213.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCP5	ENST00000718213.1		n.96-11643G>A		intron	N/A
	HCP5	ENST00000718214.1		n.96-11643G>A		intron	N/A
	HCP5	ENST00000666495.2		n.*83G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29427 AN: 151670 Hom.: 3179 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.194 AC: 29452 AN: 151792 Hom.: 3184 Cov.: 32 AF XY: 0.194 AC XY: 14419 AN XY: 74212

African (AFR) AF: 0.138 AC: 5700 AN: 41320

American (AMR) AF: 0.261 AC: 3962 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 644 AN: 3472

East Asian (EAS) AF: 0.170 AC: 873 AN: 5148

South Asian (SAS) AF: 0.207 AC: 995 AN: 4810

European-Finnish (FIN) AF: 0.164 AC: 1735 AN: 10578

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.218 AC: 14787 AN: 67952

Other (OTH) AF: 0.200 AC: 422 AN: 2108

Alfa AF: 0.209 Hom.: 14100

Bravo AF: 0.201

Asia WGS AF: 0.172 AC: 600 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.28
PhyloP100		-0.13

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2248462;

hg19: chr6-31446796;