rs6589567

Variant names:

• chr11-116799960-A-C
• rs6589567

Your query was ambiguous. Multiple possible variants found:

• chr11-116799960-A-C
• chr11-116799960-A-G
• chr11-116799960-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;