rs2523676

Variant names:

• chr6-31468214-C-T
• rs2523676
• ENST00000414046.3:n.4954C>T

Variant summary

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

The ENST00000414046.3(HCP5):​n.4954C>T 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 0.161 in 151,818 control chromosomes in the GnomAD database, including 2,398 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 0.16 (2398 hom., cov: 32)
• Consequence: HCP5 ENST00000414046.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 19 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 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.4954C>T		non_coding_transcript_exon_variant	Exon 2 of 2	4
HCP5	ENST00000467369.2	n.217+4706C>T		intron_variant	Intron 2 of 2	4
HCP5	ENST00000666495.2	n.95+4935C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24349 AN: 151700 Hom.: 2393 Cov.: 32

Gnomad AFR AF: 0.0998

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.0560

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.161 AC: 24371 AN: 151818 Hom.: 2398 Cov.: 32 AF XY: 0.162 AC XY: 12029 AN XY: 74196

African (AFR) AF: 0.0999 AC: 4134 AN: 41386

American (AMR) AF: 0.236 AC: 3589 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.0560 AC: 194 AN: 3464

East Asian (EAS) AF: 0.280 AC: 1439 AN: 5146

South Asian (SAS) AF: 0.170 AC: 818 AN: 4814

European-Finnish (FIN) AF: 0.185 AC: 1954 AN: 10558

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11860 AN: 67956

Other (OTH) AF: 0.128 AC: 269 AN: 2106

Alfa AF: 0.174 Hom.: 1778

Bravo AF: 0.160

Asia WGS AF: 0.168 AC: 586 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.57
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2523676; hg19: chr6-31435991;