rs714647

Positions:

• chr15-101512431-G-A

Variant summary

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

The variant allele was found at a frequency of 0.557 in 151,584 control chromosomes in the GnomAD database, including 24,759 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 0.56 (24759 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510

Genes affected

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.101512431G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PCSK6	ENST00000557794.5	n.123+12649C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84401 AN: 151466 Hom.: 24748 Cov.: 31

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.557 AC: 84445 AN: 151584 Hom.: 24759 Cov.: 31 AF XY: 0.559 AC XY: 41359 AN XY: 74014

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.692

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.585

Alfa AF: 0.607 Hom.: 38359

Bravo AF: 0.557

Asia WGS AF: 0.575 AC: 2000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs714647; hg19: chr15-102052634;