rs6589939

chr11-122647817-A-Gchr11-122647817-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 0.359 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.359 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

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.357

Alfa AF: 0.384 Hom.: 1883

Bravo AF: 0.353

Asia WGS AF: 0.347 AC: 1208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.4
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6589939; hg19: chr11-122518525;