rs961253

Positions:

• chr20-6423634-C-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 0.332 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;