rs3094013

Variant names:

• chr6-31466589-G-A
• rs3094013
• ENST00000414046.3:n.3329G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-31466589-G-A
• chr6-31466589-G-C
• chr6-31466589-G-T

Variant summary

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

The ENST00000414046.3(HCP5):​n.3329G>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 0.075 in 152,062 control chromosomes in the GnomAD database, including 610 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 0.075 (610 hom., cov: 32)
• Consequence: HCP5 ENST00000414046.3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 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	ENST00000414046.3	n.3329G>A		non_coding_transcript_exon_variant	Exon 2 of 2	4
HCP5	ENST00000467369.2	n.217+3081G>A		intron_variant	Intron 2 of 2	4
HCP5	ENST00000666495.2	n.95+3310G>A		intron_variant	Intron 1 of 1
HCP5	ENST00000674016.1	n.97+2459G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0751 AC: 11408 AN: 151944 Hom.: 610 Cov.: 32

Gnomad AFR AF: 0.0337

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0375

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.00522

Gnomad SAS AF: 0.0616

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0570

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

GnomAD4 genome AF: 0.0750 AC: 11410 AN: 152062 Hom.: 610 Cov.: 32 AF XY: 0.0711 AC XY: 5284 AN XY: 74352

Gnomad4 AFR AF: 0.0336

Gnomad4 AMR AF: 0.0374

Gnomad4 ASJ AF: 0.0435

Gnomad4 EAS AF: 0.00504

Gnomad4 SAS AF: 0.0627

Gnomad4 FIN AF: 0.0781

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.0565

Alfa AF: 0.101 Hom.: 576

Bravo AF: 0.0688

Asia WGS AF: 0.0220 AC: 78 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.3
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3094013; hg19: chr6-31434366;