11-636689-G-C

Variant names:

• chr11-636689-G-C
• rs747302

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 0.539 in 139,460 control chromosomes in the GnomAD database, including 19,471 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 0.54 (19471 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280
• Publications: 60 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.584 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: 0.539 AC: 75062 AN: 139340 Hom.: 19445 Cov.: 25

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.474

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.539 AC: 75142 AN: 139460 Hom.: 19471 Cov.: 25 AF XY: 0.540 AC XY: 36607 AN XY: 67778

African (AFR) AF: 0.455 AC: 16445 AN: 36138

American (AMR) AF: 0.509 AC: 7006 AN: 13764

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1397 AN: 3232

East Asian (EAS) AF: 0.422 AC: 1884 AN: 4466

South Asian (SAS) AF: 0.576 AC: 2484 AN: 4314

European-Finnish (FIN) AF: 0.629 AC: 6152 AN: 9776

Middle Eastern (MID) AF: 0.468 AC: 132 AN: 282

European-Non Finnish (NFE) AF: 0.589 AC: 38102 AN: 64732

Other (OTH) AF: 0.538 AC: 1022 AN: 1900

Alfa AF: 0.392 Hom.: 1094

Bravo AF: 0.484

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.5
DANN	Benign	0.71
PhyloP100		0.028

Splicing

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

Other links and lift over

dbSNP: rs747302; hg19: chr11-636689; COSMIC: COSV51562359;