rs2248462

Variant names:

• chr6-31479019-G-A
• rs2248462
• ENST00000666495.2:n.*83G>A

Variant summary

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

The ENST00000666495.2(HCP5):​n.*83G>A variant causes a downstream gene 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 ENST00000666495.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.254 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	ENST00000666495.2	n.*83G>A		downstream_gene_variant

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

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.200

Alfa AF: 0.215 Hom.: 5528

Bravo AF: 0.201

Asia WGS AF: 0.172 AC: 600 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2248462; hg19: chr6-31446796;