rs2596450

Positions:

• 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 ENST00000666495.2(HCP5):​n.96-6561G>A variant causes a intron, non coding transcript 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 ENST00000666495.2 intron, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HCP5	ENST00000666495.2	n.96-6561G>A		intron_variant, non_coding_transcript_variant
HCP5	ENST00000414046.3	n.7206G>A		non_coding_transcript_exon_variant	2/2	4
HCP5	ENST00000467369.2	n.218-6561G>A		intron_variant, non_coding_transcript_variant		4
HCP5	ENST00000674016.1	n.97+6336G>A		intron_variant, non_coding_transcript_variant

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;