11-641191-C-A

Variant names:

• chr11-641191-C-A
• rs11246226

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 0.48 in 152,170 control chromosomes in the GnomAD database, including 17,968 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 0.48 (17968 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.864
• Publications: 43 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 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: 0.480 AC: 73011 AN: 152052 Hom.: 17958 Cov.: 35

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.480 AC: 73065 AN: 152170 Hom.: 17968 Cov.: 35 AF XY: 0.483 AC XY: 35956 AN XY: 74396

African (AFR) AF: 0.380 AC: 15777 AN: 41538

American (AMR) AF: 0.526 AC: 8053 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1682 AN: 3470

East Asian (EAS) AF: 0.730 AC: 3757 AN: 5150

South Asian (SAS) AF: 0.585 AC: 2827 AN: 4830

European-Finnish (FIN) AF: 0.474 AC: 5027 AN: 10596

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34292 AN: 67964

Other (OTH) AF: 0.476 AC: 1005 AN: 2112

Alfa AF: 0.468 Hom.: 25322

Bravo AF: 0.479

Asia WGS AF: 0.616 AC: 2142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.0
DANN	Benign	0.87
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs11246226; hg19: chr11-641191;