rs2649663

Variant names:

• chr11-57589832-G-A
• rs2649663

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 0.813 in 152,214 control chromosomes in the GnomAD database, including 50,639 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 0.81 (50639 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 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: 0.813 AC: 123687 AN: 152096 Hom.: 50595 Cov.: 33

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.813 AC: 123785 AN: 152214 Hom.: 50639 Cov.: 33 AF XY: 0.815 AC XY: 60670 AN XY: 74432

African (AFR) AF: 0.886 AC: 36835 AN: 41558

American (AMR) AF: 0.769 AC: 11759 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.840 AC: 2914 AN: 3470

East Asian (EAS) AF: 0.868 AC: 4499 AN: 5184

South Asian (SAS) AF: 0.775 AC: 3739 AN: 4826

European-Finnish (FIN) AF: 0.805 AC: 8518 AN: 10586

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.777 AC: 52845 AN: 67990

Other (OTH) AF: 0.800 AC: 1689 AN: 2110

Alfa AF: 0.808 Hom.: 8772

Bravo AF: 0.813

Asia WGS AF: 0.817 AC: 2840 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	0.51
PhyloP100		-0.032

Splicing

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

Other links and lift over

dbSNP: rs2649663; hg19: chr11-57357305;