11-3238579-G-A

Variant names:

• chr11-3238579-G-A
• rs11026091

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 0.436 in 152,076 control chromosomes in the GnomAD database, including 14,727 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 0.44 (14727 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66299 AN: 151958 Hom.: 14739 Cov.: 33

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.436 AC: 66302 AN: 152076 Hom.: 14727 Cov.: 33 AF XY: 0.431 AC XY: 32068 AN XY: 74340

African (AFR) AF: 0.395 AC: 16395 AN: 41468

American (AMR) AF: 0.363 AC: 5550 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1787 AN: 3470

East Asian (EAS) AF: 0.628 AC: 3252 AN: 5180

South Asian (SAS) AF: 0.370 AC: 1785 AN: 4822

European-Finnish (FIN) AF: 0.430 AC: 4537 AN: 10548

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31476 AN: 67992

Other (OTH) AF: 0.453 AC: 955 AN: 2108

Alfa AF: 0.453 Hom.: 67313

Bravo AF: 0.430

Asia WGS AF: 0.474 AC: 1649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.3
DANN	Benign	0.66
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs11026091; hg19: chr11-3259809;