chr6-31467342-G-A

Variant names:

• chr6-31467342-G-A
• rs2516518
• ENST00000414046.3:n.4082G>A

Variant summary

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

The ENST00000414046.3(HCP5):​n.4082G>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 0.125 in 151,708 control chromosomes in the GnomAD database, including 1,723 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 0.12 (1723 hom., cov: 32)
• Consequence: HCP5 ENST00000414046.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• Publications: 6 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 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.4082G>A		non_coding_transcript_exon_variant	Exon 2 of 2	4
HCP5	ENST00000467369.2	n.217+3834G>A		intron_variant	Intron 2 of 2	4
HCP5	ENST00000666495.2	n.95+4063G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18909 AN: 151590 Hom.: 1722 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.0363

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.0164

Gnomad SAS AF: 0.0157

Gnomad FIN AF: 0.0103

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0928

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.125 AC: 18926 AN: 151708 Hom.: 1723 Cov.: 32 AF XY: 0.118 AC XY: 8768 AN XY: 74166

African (AFR) AF: 0.216 AC: 8915 AN: 41190

American (AMR) AF: 0.157 AC: 2381 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 638 AN: 3468

East Asian (EAS) AF: 0.0165 AC: 85 AN: 5166

South Asian (SAS) AF: 0.0158 AC: 76 AN: 4822

European-Finnish (FIN) AF: 0.0103 AC: 109 AN: 10586

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.0928 AC: 6308 AN: 67972

Other (OTH) AF: 0.166 AC: 351 AN: 2110

Alfa AF: 0.110 Hom.: 1592

Bravo AF: 0.146

Asia WGS AF: 0.0360 AC: 127 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.6
DANN	Benign	0.53
PhyloP100		-0.41
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2516518; hg19: chr6-31435119;