11-38566720-G-A

Variant names:

• chr11-38566720-G-A
• rs10837012

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 0.769 in 151,818 control chromosomes in the GnomAD database, including 48,931 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 0.77 (48931 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116653 AN: 151702 Hom.: 48925 Cov.: 31

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.947

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.802

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

GnomAD4 genome AF: 0.769 AC: 116698 AN: 151818 Hom.: 48931 Cov.: 31 AF XY: 0.768 AC XY: 57000 AN XY: 74178

African (AFR) AF: 0.414 AC: 17098 AN: 41348

American (AMR) AF: 0.824 AC: 12536 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.947 AC: 3286 AN: 3470

East Asian (EAS) AF: 0.642 AC: 3282 AN: 5116

South Asian (SAS) AF: 0.742 AC: 3574 AN: 4818

European-Finnish (FIN) AF: 0.922 AC: 9763 AN: 10592

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.947 AC: 64362 AN: 67952

Other (OTH) AF: 0.798 AC: 1683 AN: 2108

Alfa AF: 0.871 Hom.: 14740

Bravo AF: 0.746

Asia WGS AF: 0.648 AC: 2245 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.8
DANN	Benign	0.21
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs10837012; hg19: chr11-38588270;