11-92991185-T-C

Variant names:

• chr11-92991185-T-C
• rs7121092

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 0.558 in 151,610 control chromosomes in the GnomAD database, including 23,929 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 0.56 (23929 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84525 AN: 151488 Hom.: 23897 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.574

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.558 AC: 84622 AN: 151610 Hom.: 23929 Cov.: 32 AF XY: 0.566 AC XY: 41964 AN XY: 74094

African (AFR) AF: 0.561 AC: 23214 AN: 41350

American (AMR) AF: 0.657 AC: 10016 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1524 AN: 3466

East Asian (EAS) AF: 0.697 AC: 3583 AN: 5138

South Asian (SAS) AF: 0.687 AC: 3300 AN: 4802

European-Finnish (FIN) AF: 0.576 AC: 6072 AN: 10544

Middle Eastern (MID) AF: 0.576 AC: 167 AN: 290

European-Non Finnish (NFE) AF: 0.516 AC: 34980 AN: 67764

Other (OTH) AF: 0.544 AC: 1145 AN: 2106

Alfa AF: 0.548 Hom.: 8441

Bravo AF: 0.565

Asia WGS AF: 0.651 AC: 2262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.6
DANN	Benign	0.85
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs7121092; hg19: chr11-92724351;