rs651933

Variant names:

• chr11-72215616-G-A
• rs651933

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 0.52 in 152,030 control chromosomes in the GnomAD database, including 21,606 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 0.52 (21606 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.695 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: 0.519 AC: 78907 AN: 151912 Hom.: 21557 Cov.: 33

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.520 AC: 79012 AN: 152030 Hom.: 21606 Cov.: 33 AF XY: 0.523 AC XY: 38892 AN XY: 74308

African (AFR) AF: 0.702 AC: 29099 AN: 41452

American (AMR) AF: 0.388 AC: 5927 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2012 AN: 3470

East Asian (EAS) AF: 0.473 AC: 2453 AN: 5184

South Asian (SAS) AF: 0.551 AC: 2651 AN: 4810

European-Finnish (FIN) AF: 0.503 AC: 5315 AN: 10558

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30014 AN: 67966

Other (OTH) AF: 0.500 AC: 1056 AN: 2112

Alfa AF: 0.466 Hom.: 72970

Bravo AF: 0.514

Asia WGS AF: 0.564 AC: 1964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.47
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs651933; hg19: chr11-71926660;