rs11124858

Variant names:

• chr2-42033184-A-G
• rs11124858

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 0.422 in 151,772 control chromosomes in the GnomAD database, including 14,054 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 (14054 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.517 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: 0.421 AC: 63873 AN: 151654 Hom.: 14015 Cov.: 31

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.422 AC: 63974 AN: 151772 Hom.: 14054 Cov.: 31 AF XY: 0.422 AC XY: 31266 AN XY: 74142

African (AFR) AF: 0.523 AC: 21620 AN: 41336

American (AMR) AF: 0.527 AC: 8042 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1399 AN: 3464

East Asian (EAS) AF: 0.407 AC: 2086 AN: 5124

South Asian (SAS) AF: 0.388 AC: 1866 AN: 4810

European-Finnish (FIN) AF: 0.317 AC: 3335 AN: 10520

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24131 AN: 67930

Other (OTH) AF: 0.423 AC: 894 AN: 2114

Alfa AF: 0.374 Hom.: 5731

Bravo AF: 0.446

Asia WGS AF: 0.405 AC: 1409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.30
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs11124858; hg19: chr2-42260324;