6-31470466-G-A

Variant names:

• chr6-31470466-G-A
• rs2596450
• ENST00000414046.3:n.7206G>A

Variant summary

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

The ENST00000414046.3(HCP5):​n.7206G>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 0.703 in 151,396 control chromosomes in the GnomAD database, including 38,049 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 0.70 (38049 hom., cov: 30)
• Consequence: HCP5 ENST00000414046.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206
• Publications: 5 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 (EAS) allele frequency at 95% confidence interval = 0.868 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCP5	ENST00000414046.3	TSL:4	n.7206G>A		non_coding_transcript_exon	Exon 2 of 2
	HCP5	ENST00000467369.2	TSL:4	n.218-6561G>A		intron	N/A
	HCP5	ENST00000666495.2		n.96-6561G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106368 AN: 151278 Hom.: 38011 Cov.: 30

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.703 AC: 106462 AN: 151396 Hom.: 38049 Cov.: 30 AF XY: 0.699 AC XY: 51729 AN XY: 73974

African (AFR) AF: 0.733 AC: 30163 AN: 41152

American (AMR) AF: 0.773 AC: 11747 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2689 AN: 3466

East Asian (EAS) AF: 0.890 AC: 4567 AN: 5134

South Asian (SAS) AF: 0.736 AC: 3451 AN: 4686

European-Finnish (FIN) AF: 0.546 AC: 5760 AN: 10548

Middle Eastern (MID) AF: 0.717 AC: 208 AN: 290

European-Non Finnish (NFE) AF: 0.674 AC: 45781 AN: 67914

Other (OTH) AF: 0.731 AC: 1539 AN: 2104

Alfa AF: 0.694 Hom.: 5234

Bravo AF: 0.724

Asia WGS AF: 0.782 AC: 2718 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.46
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs2596450; hg19: chr6-31438243;