rs961253

Variant names:

• chr20-6423634-C-A
• rs961253

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 0.332 in 151,762 control chromosomes in the GnomAD database, including 8,643 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 0.33 (8643 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.759

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.349 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: 0.332 AC: 50406 AN: 151646 Hom.: 8642 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.0942

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.332 AC: 50430 AN: 151762 Hom.: 8643 Cov.: 32 AF XY: 0.330 AC XY: 24448 AN XY: 74142

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.0944

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.331

Alfa AF: 0.339 Hom.: 18851

Bravo AF: 0.331

Asia WGS AF: 0.246 AC: 856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.8
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs961253; hg19: chr20-6404281;