rs3094014

Variant names:

• chr6-31465781-G-A
• rs3094014
• ENST00000414046.3:n.2521G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-31465781-G-A
• chr6-31465781-G-C
• chr6-31465781-G-T

Variant summary

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

The ENST00000414046.3(HCP5):​n.2521G>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 ENST00000414046.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 33 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=-0.92).
• 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 rank	MANE	Protein	UniProt
HCP5	NR_040662.1	n.2511G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCP5	ENST00000414046.3	n.2521G>A		non_coding_transcript_exon_variant	Exon 2 of 2	4
HCP5	ENST00000670109.1	n.2484G>A		non_coding_transcript_exon_variant	Exon 2 of 2
HCP5	ENST00000467369.2	n.217+2273G>A		intron_variant	Intron 2 of 2	4

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 18

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.167 AC: 6924 AN: 41348

American (AMR) AF: 0.126 AC: 1927 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3468

East Asian (EAS) AF: 0.164 AC: 847 AN: 5158

South Asian (SAS) AF: 0.282 AC: 1359 AN: 4812

European-Finnish (FIN) AF: 0.126 AC: 1337 AN: 10576

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.177 AC: 12044 AN: 67998

Other (OTH) AF: 0.161 AC: 339 AN: 2108

Alfa AF: 0.169 Hom.: 5555

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
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs3094014; hg19: chr6-31433558;