rs3094013

chr6-31466589-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+3310G>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 0.075 in 152,062 control chromosomes in the GnomAD database, including 610 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 0.075 (610 hom., cov: 32)
• Consequence: HCP5 ENST00000666495.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211

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 (NFE) allele frequency at 95% confidence interval = 0.114 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+3310G>A		intron_variant, non_coding_transcript_variant
HCP5	ENST00000414046.3	n.3329G>A		non_coding_transcript_exon_variant	2/2	4
HCP5	ENST00000467369.2	n.217+3081G>A		intron_variant, non_coding_transcript_variant		4
HCP5	ENST00000674016.1	n.97+2459G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0751 AC: 11408 AN: 151944 Hom.: 610 Cov.: 32

Gnomad AFR AF: 0.0337

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0375

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.00522

Gnomad SAS AF: 0.0616

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0570

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

GnomAD4 genome AF: 0.0750 AC: 11410 AN: 152062 Hom.: 610 Cov.: 32 AF XY: 0.0711 AC XY: 5284 AN XY: 74352

Gnomad4 AFR AF: 0.0336

Gnomad4 AMR AF: 0.0374

Gnomad4 ASJ AF: 0.0435

Gnomad4 EAS AF: 0.00504

Gnomad4 SAS AF: 0.0627

Gnomad4 FIN AF: 0.0781

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.0565

Alfa AF: 0.101 Hom.: 576

Bravo AF: 0.0688

Asia WGS AF: 0.0220 AC: 78 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	8.3
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3094013; hg19: chr6-31434366;