11-636199-C-T

Variant names:

• chr11-636199-C-T
• rs936460

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 0.694 in 151,952 control chromosomes in the GnomAD database, including 36,897 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 0.69 (36897 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 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: 0.694 AC: 105306 AN: 151834 Hom.: 36852 Cov.: 31

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.694 AC: 105408 AN: 151952 Hom.: 36897 Cov.: 31 AF XY: 0.702 AC XY: 52081 AN XY: 74234

African (AFR) AF: 0.617 AC: 25557 AN: 41424

American (AMR) AF: 0.708 AC: 10797 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2590 AN: 3464

East Asian (EAS) AF: 0.931 AC: 4783 AN: 5140

South Asian (SAS) AF: 0.863 AC: 4167 AN: 4826

European-Finnish (FIN) AF: 0.753 AC: 7950 AN: 10558

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47156 AN: 67966

Other (OTH) AF: 0.721 AC: 1522 AN: 2110

Alfa AF: 0.640 Hom.: 4942

Bravo AF: 0.686

Asia WGS AF: 0.874 AC: 3041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.69
DANN	Benign	0.77
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs936460; hg19: chr11-636199;