rs961746

chr11-20139419-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 0.418 in 151,832 control chromosomes in the GnomAD database, including 13,533 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 0.42 (13533 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.485 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: 0.418 AC: 63441 AN: 151714 Hom.: 13513 Cov.: 33

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.418 AC: 63496 AN: 151832 Hom.: 13533 Cov.: 33 AF XY: 0.423 AC XY: 31401 AN XY: 74172

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.386

Alfa AF: 0.370 Hom.: 10523

Bravo AF: 0.421

Asia WGS AF: 0.413 AC: 1436 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.45
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs961746; hg19: chr11-20160965;