11-33892881-G-A

Variant names:

• chr11-33892881-G-A
• rs3758640

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 0.64 in 152,080 control chromosomes in the GnomAD database, including 31,198 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 0.64 (31198 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 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: 0.640 AC: 97212 AN: 151962 Hom.: 31184 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.640 AC: 97279 AN: 152080 Hom.: 31198 Cov.: 32 AF XY: 0.641 AC XY: 47624 AN XY: 74348

African (AFR) AF: 0.650 AC: 26941 AN: 41472

American (AMR) AF: 0.583 AC: 8916 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2065 AN: 3470

East Asian (EAS) AF: 0.674 AC: 3483 AN: 5170

South Asian (SAS) AF: 0.611 AC: 2944 AN: 4818

European-Finnish (FIN) AF: 0.698 AC: 7378 AN: 10566

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43342 AN: 67976

Other (OTH) AF: 0.629 AC: 1330 AN: 2114

Alfa AF: 0.633 Hom.: 58484

Bravo AF: 0.634

Asia WGS AF: 0.615 AC: 2136 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.51
DANN	Benign	0.50
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs3758640; hg19: chr11-33914428;