rs2523674

Variant names:

• chr6-31469012-A-G
• rs2523674
• ENST00000414046.3:n.5752A>G

Variant summary

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

The ENST00000414046.3(HCP5):​n.5752A>G 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 0.539 in 151,618 control chromosomes in the GnomAD database, including 23,119 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 0.54 (23119 hom., cov: 33)
• Consequence: HCP5 ENST00000414046.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144
• Publications: 28 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.659 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.5752A>G		non_coding_transcript_exon_variant	Exon 2 of 2	4
HCP5	ENST00000467369.2	n.217+5504A>G		intron_variant	Intron 2 of 2	4
HCP5	ENST00000666495.2	n.95+5733A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81606 AN: 151498 Hom.: 23077 Cov.: 33

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.539 AC: 81703 AN: 151618 Hom.: 23119 Cov.: 33 AF XY: 0.533 AC XY: 39498 AN XY: 74114

African (AFR) AF: 0.666 AC: 27426 AN: 41196

American (AMR) AF: 0.562 AC: 8546 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2417 AN: 3460

East Asian (EAS) AF: 0.579 AC: 2983 AN: 5156

South Asian (SAS) AF: 0.559 AC: 2686 AN: 4806

European-Finnish (FIN) AF: 0.350 AC: 3692 AN: 10562

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32190 AN: 67926

Other (OTH) AF: 0.599 AC: 1263 AN: 2110

Alfa AF: 0.509 Hom.: 25038

Bravo AF: 0.563

Asia WGS AF: 0.607 AC: 2110 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.0
DANN	Benign	0.54
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2523674; hg19: chr6-31436789;