11-102536460-T-C

Variant names:

• chr11-102536460-T-C
• rs1943779

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 0.294 in 152,110 control chromosomes in the GnomAD database, including 6,760 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 0.29 (6760 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 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: 0.294 AC: 44706 AN: 151992 Hom.: 6755 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.0728

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.294 AC: 44735 AN: 152110 Hom.: 6760 Cov.: 32 AF XY: 0.293 AC XY: 21790 AN XY: 74376

African (AFR) AF: 0.331 AC: 13718 AN: 41482

American (AMR) AF: 0.270 AC: 4137 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 960 AN: 3470

East Asian (EAS) AF: 0.0726 AC: 376 AN: 5182

South Asian (SAS) AF: 0.321 AC: 1547 AN: 4822

European-Finnish (FIN) AF: 0.266 AC: 2813 AN: 10584

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20128 AN: 67962

Other (OTH) AF: 0.302 AC: 635 AN: 2106

Alfa AF: 0.284 Hom.: 5787

Bravo AF: 0.295

Asia WGS AF: 0.234 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.94
DANN	Benign	0.81
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1943779; hg19: chr11-102407191;