11-92909231-C-T

Variant names:

• chr11-92909231-C-T
• rs10501799

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 0.42 in 151,944 control chromosomes in the GnomAD database, including 13,898 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 0.42 (13898 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63731 AN: 151826 Hom.: 13852 Cov.: 32

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.420 AC: 63849 AN: 151944 Hom.: 13898 Cov.: 32 AF XY: 0.422 AC XY: 31339 AN XY: 74252

African (AFR) AF: 0.484 AC: 20044 AN: 41442

American (AMR) AF: 0.512 AC: 7816 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1199 AN: 3462

East Asian (EAS) AF: 0.523 AC: 2693 AN: 5154

South Asian (SAS) AF: 0.472 AC: 2269 AN: 4812

European-Finnish (FIN) AF: 0.373 AC: 3936 AN: 10542

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24424 AN: 67948

Other (OTH) AF: 0.415 AC: 875 AN: 2106

Alfa AF: 0.399 Hom.: 1888

Bravo AF: 0.436

Asia WGS AF: 0.533 AC: 1849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.017
DANN	Benign	0.57
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10501799; hg19: chr11-92642397;