rs6589567

chr11-116799960-A-Cchr11-116799960-A-Gchr11-116799960-A-T

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 0.87 in 150,824 control chromosomes in the GnomAD database, including 57,569 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 0.87 (57569 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.906 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: 0.870 AC: 131174 AN: 150708 Hom.: 57525 Cov.: 31

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.841

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.866

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

GnomAD4 genome AF: 0.870 AC: 131270 AN: 150824 Hom.: 57569 Cov.: 31 AF XY: 0.864 AC XY: 63691 AN XY: 73724

Gnomad4 AFR AF: 0.914

Gnomad4 AMR AF: 0.823

Gnomad4 ASJ AF: 0.858

Gnomad4 EAS AF: 0.718

Gnomad4 SAS AF: 0.757

Gnomad4 FIN AF: 0.824

Gnomad4 NFE AF: 0.883

Gnomad4 OTH AF: 0.861

Alfa AF: 0.867 Hom.: 29179

Bravo AF: 0.876

Asia WGS AF: 0.732 AC: 2546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	1.1
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6589567; hg19: chr11-116670676;