11-124852181-T-C

Variant names:

• chr11-124852181-T-C
• rs725291

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 0.262 in 152,120 control chromosomes in the GnomAD database, including 5,338 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 0.26 (5338 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 1 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 (SAS) allele frequency at 95% confidence interval = 0.288 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: 0.262 AC: 39801 AN: 152002 Hom.: 5332 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.0719

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.262 AC: 39840 AN: 152120 Hom.: 5338 Cov.: 32 AF XY: 0.262 AC XY: 19492 AN XY: 74366

African (AFR) AF: 0.293 AC: 12144 AN: 41478

American (AMR) AF: 0.261 AC: 3986 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 943 AN: 3468

East Asian (EAS) AF: 0.0716 AC: 372 AN: 5192

South Asian (SAS) AF: 0.297 AC: 1430 AN: 4818

European-Finnish (FIN) AF: 0.281 AC: 2978 AN: 10580

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 17014 AN: 67986

Other (OTH) AF: 0.267 AC: 562 AN: 2108

Alfa AF: 0.258 Hom.: 634

Bravo AF: 0.259

Asia WGS AF: 0.196 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.66
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs725291; hg19: chr11-124722077;