rs6589939

Variant names:

• chr11-122647817-A-G
• rs6589939

Your query was ambiguous. Multiple possible variants found:

• chr11-122647817-A-G
• chr11-122647817-A-T

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 0.359 in 151,914 control chromosomes in the GnomAD database, including 10,059 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 0.36 (10059 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54556 AN: 151796 Hom.: 10047 Cov.: 31

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.359 AC: 54605 AN: 151914 Hom.: 10059 Cov.: 31 AF XY: 0.356 AC XY: 26421 AN XY: 74250

African (AFR) AF: 0.351 AC: 14541 AN: 41406

American (AMR) AF: 0.356 AC: 5434 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 850 AN: 3468

East Asian (EAS) AF: 0.189 AC: 973 AN: 5158

South Asian (SAS) AF: 0.383 AC: 1846 AN: 4824

European-Finnish (FIN) AF: 0.355 AC: 3743 AN: 10558

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26174 AN: 67936

Other (OTH) AF: 0.357 AC: 753 AN: 2110

Alfa AF: 0.373 Hom.: 3376

Bravo AF: 0.353

Asia WGS AF: 0.347 AC: 1208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.62
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs6589939; hg19: chr11-122518525;