6-31478132-A-G

Position:

• chr6-31478132-A-G

Variant summary

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

The ENST00000666495.2(HCP5):​n.1201A>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 0.339 in 151,452 control chromosomes in the GnomAD database, including 9,115 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 0.34 (9115 hom., cov: 31)
• Consequence: HCP5 ENST00000666495.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.653

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 (EAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HCP5	ENST00000666495.2	n.1201A>G		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51290 AN: 151336 Hom.: 9105 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.339 AC: 51324 AN: 151452 Hom.: 9115 Cov.: 31 AF XY: 0.337 AC XY: 24978 AN XY: 74018

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.324

Alfa AF: 0.347 Hom.: 6090

Bravo AF: 0.343

Asia WGS AF: 0.472 AC: 1639 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	4.6
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2395488; hg19: chr6-31445909;