rs2649663

Positions:

• chr11-57589832-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 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. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency: Genomes: 𝑓 0.81 (50639 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BP6: Variant 11-57589832-G-A is Benign according to our data. Variant chr11-57589832-G-A is described in Lovd as [Likely_benign].
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.769

Gnomad4 ASJ AF: 0.840

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.775

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.777

Gnomad4 OTH AF: 0.800

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2649663; hg19: chr11-57357305;