rs2596450

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr6-31470466-G-A
• chr6-31470466-G-C
• chr6-31470466-G-T

Variant summary

Our verdict is Benign. Variant got -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

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 (EAS) allele frequency at 95% confidence interval = 0.868 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.7206G>A		non_coding_transcript_exon_variant	Exon 2 of 2	4
HCP5	ENST00000467369.2	n.218-6561G>A		intron_variant	Intron 2 of 2	4
HCP5	ENST00000666495.2	n.96-6561G>A		intron_variant	Intron 1 of 1
HCP5	ENST00000674016.1	n.97+6336G>A		intron_variant	Intron 1 of 1

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

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.890

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.731

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2596450; hg19: chr6-31438243;