11-37162788-C-T

Variant names:

• chr11-37162788-C-T
• rs10836699

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 0.326 in 146,668 control chromosomes in the GnomAD database, including 9,725 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 0.33 (9725 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 4 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 = 0.453 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: 0.326 AC: 47874 AN: 146632 Hom.: 9730 Cov.: 28

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.0807

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.530

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.326 AC: 47869 AN: 146668 Hom.: 9725 Cov.: 28 AF XY: 0.318 AC XY: 22601 AN XY: 70974

African (AFR) AF: 0.105 AC: 4187 AN: 40008

American (AMR) AF: 0.376 AC: 5450 AN: 14488

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1603 AN: 3444

East Asian (EAS) AF: 0.0813 AC: 397 AN: 4882

South Asian (SAS) AF: 0.289 AC: 1354 AN: 4688

European-Finnish (FIN) AF: 0.319 AC: 2764 AN: 8674

Middle Eastern (MID) AF: 0.528 AC: 149 AN: 282

European-Non Finnish (NFE) AF: 0.457 AC: 30766 AN: 67258

Other (OTH) AF: 0.387 AC: 788 AN: 2038

Alfa AF: 0.424 Hom.: 16123

Bravo AF: 0.317

Asia WGS AF: 0.185 AC: 644 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.39
DANN	Benign	0.33
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10836699; hg19: chr11-37184338;