rs11126184

Variant names:

• chr2-68425042-C-A
• rs11126184

Your query was ambiguous. Multiple possible variants found:

• chr2-68425042-C-A
• chr2-68425042-C-G
• chr2-68425042-C-T

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 0.561 in 151,824 control chromosomes in the GnomAD database, including 25,475 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 (25475 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• Publications: 6 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 = 0.84 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: 0.561 AC: 85160 AN: 151704 Hom.: 25462 Cov.: 30

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.561 AC: 85200 AN: 151824 Hom.: 25475 Cov.: 30 AF XY: 0.565 AC XY: 41942 AN XY: 74170

African (AFR) AF: 0.348 AC: 14391 AN: 41370

American (AMR) AF: 0.663 AC: 10114 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2543 AN: 3470

East Asian (EAS) AF: 0.861 AC: 4445 AN: 5164

South Asian (SAS) AF: 0.682 AC: 3277 AN: 4806

European-Finnish (FIN) AF: 0.608 AC: 6411 AN: 10550

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.618 AC: 41970 AN: 67898

Other (OTH) AF: 0.626 AC: 1323 AN: 2112

Alfa AF: 0.540 Hom.: 3489

Bravo AF: 0.558

Asia WGS AF: 0.770 AC: 2676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.6
DANN	Benign	0.66
PhyloP100		-0.047

Splicing

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

Other links and lift over

dbSNP: rs11126184; hg19: chr2-68652174; COSMIC: COSV66487076;