rs662968

Variant names:

• chr15-49716246-G-A
• rs662968

Your query was ambiguous. Multiple possible variants found:

• chr15-49716246-G-A
• chr15-49716246-G-C

Variant summary

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

The variant allele was found at a frequency of 0.568 in 151,852 control chromosomes in the GnomAD database, including 24,754 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 0.57 (24754 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.499
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 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

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86107 AN: 151732 Hom.: 24718 Cov.: 31

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.568 AC: 86196 AN: 151852 Hom.: 24754 Cov.: 31 AF XY: 0.562 AC XY: 41658 AN XY: 74164

African (AFR) AF: 0.636 AC: 26335 AN: 41398

American (AMR) AF: 0.495 AC: 7554 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1868 AN: 3470

East Asian (EAS) AF: 0.493 AC: 2543 AN: 5156

South Asian (SAS) AF: 0.599 AC: 2879 AN: 4804

European-Finnish (FIN) AF: 0.486 AC: 5099 AN: 10498

Middle Eastern (MID) AF: 0.586 AC: 171 AN: 292

European-Non Finnish (NFE) AF: 0.558 AC: 37933 AN: 67966

Other (OTH) AF: 0.562 AC: 1183 AN: 2104

Alfa AF: 0.541 Hom.: 12889

Bravo AF: 0.568

Asia WGS AF: 0.569 AC: 1975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.5
DANN	Benign	0.29
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs662968; hg19: chr15-50008443;