rs3094014

chr6-31465781-G-Achr6-31465781-G-T

Variant summary

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

The NR_040662.1(HCP5):n.2511G>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 0.167 in 151,916 control chromosomes in the GnomAD database, including 2,390 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 0.17 (2390 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: HCP5 NR_040662.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HCP5	NR_040662.1	n.2511G>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+2502G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25390 AN: 151798 Hom.: 2389 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.161

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 18 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 10

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.167 AC: 25401 AN: 151916 Hom.: 2390 Cov.: 32 AF XY: 0.167 AC XY: 12374 AN XY: 74294

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.161

Alfa AF: 0.170 Hom.: 1965

Bravo AF: 0.163

Asia WGS AF: 0.230 AC: 796 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.91
Dann	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3094014; hg19: chr6-31433558;