rs2516518

chr6-31467342-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000666495.2(HCP5):n.95+4063G>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 0.125 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 ENST00000666495.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412

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=-0.93).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCP5	ENST00000666495.2	n.95+4063G>A		intron_variant, non_coding_transcript_variant
HCP5	ENST00000414046.3	n.4082G>A		non_coding_transcript_exon_variant	2/2	4
HCP5	ENST00000467369.2	n.217+3834G>A		intron_variant, non_coding_transcript_variant		4
HCP5	ENST00000674016.1	n.97+3212G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.0165

Gnomad4 SAS AF: 0.0158

Gnomad4 FIN AF: 0.0103

Gnomad4 NFE AF: 0.0928

Gnomad4 OTH AF: 0.166

Alfa AF: 0.104 Hom.: 652

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2516518; hg19: chr6-31435119;