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. The variant received -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
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414046.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCP5	ENST00000414046.3	TSL:4	n.3329G>A		non_coding_transcript_exon	Exon 2 of 2
	HCP5	ENST00000467369.2	TSL:4	n.217+3081G>A		intron	N/A
	HCP5	ENST00000666495.2		n.95+3310G>A		intron	N/A

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

African (AFR) AF: 0.0336 AC: 1393 AN: 41418

American (AMR) AF: 0.0374 AC: 570 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0435 AC: 151 AN: 3468

East Asian (EAS) AF: 0.00504 AC: 26 AN: 5158

South Asian (SAS) AF: 0.0627 AC: 303 AN: 4830

European-Finnish (FIN) AF: 0.0781 AC: 829 AN: 10618

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7876 AN: 68004

Other (OTH) AF: 0.0565 AC: 119 AN: 2108

Alfa AF: 0.104 Hom.: 2982

Bravo AF: 0.0688

Asia WGS AF: 0.0220 AC: 78 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.3
DANN	Benign	0.31
PhyloP100		0.21
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: rs3094013; hg19: chr6-31434366;