rs2263318

chr6-31464229-G-A

Variant summary

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

The NR_040662.1(HCP5):n.959G>A 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 0.0858 in 185,098 control chromosomes in the GnomAD database, including 1,018 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 0.095 (964 hom., cov: 32)
  • Exomes 𝑓: 0.042 (54 hom.)
• Consequence: HCP5 NR_040662.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HCP5	NR_040662.1	n.959G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCP5	ENST00000666495.2	n.95+950G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0954 AC: 14497 AN: 151894 Hom.: 964 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.0164

Gnomad SAS AF: 0.0110

Gnomad FIN AF: 0.0101

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0773

Gnomad OTH AF: 0.121

GnomAD4 exome AF: 0.0422 AC: 1396 AN: 33086 Hom.: 54 Cov.: 0 AF XY: 0.0390 AC XY: 742 AN XY: 19034

Gnomad4 AFR exome AF: 0.142

Gnomad4 AMR exome AF: 0.0971

Gnomad4 ASJ exome AF: 0.130

Gnomad4 EAS exome AF: 0.0286

Gnomad4 SAS exome AF: 0.0114

Gnomad4 FIN exome AF: 0.0138

Gnomad4 NFE exome AF: 0.0542

Gnomad4 OTH exome AF: 0.0385

GnomAD4 genome AF: 0.0953 AC: 14494 AN: 152012 Hom.: 964 Cov.: 32 AF XY: 0.0905 AC XY: 6730 AN XY: 74338

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.0164

Gnomad4 SAS AF: 0.0108

Gnomad4 FIN AF: 0.0101

Gnomad4 NFE AF: 0.0773

Gnomad4 OTH AF: 0.119

Alfa AF: 0.0901 Hom.: 124

Bravo AF: 0.110

Asia WGS AF: 0.0290 AC: 101 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	8.6
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2263318; hg19: chr6-31432006;