rs662968

chr15-49716246-G-Achr15-49716246-G-C

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 0.568 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.562

Alfa AF: 0.539 Hom.: 11575

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs662968; hg19: chr15-50008443;