rs11124178

Variant names:

• chr2-239042839-G-A
• rs11124178

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 0.295 in 152,026 control chromosomes in the GnomAD database, including 7,672 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 0.29 (7672 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 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: 0.295 AC: 44741 AN: 151908 Hom.: 7660 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.0427

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.295 AC: 44782 AN: 152026 Hom.: 7672 Cov.: 32 AF XY: 0.289 AC XY: 21474 AN XY: 74314

African (AFR) AF: 0.466 AC: 19299 AN: 41430

American (AMR) AF: 0.208 AC: 3174 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 636 AN: 3464

East Asian (EAS) AF: 0.0424 AC: 220 AN: 5184

South Asian (SAS) AF: 0.181 AC: 871 AN: 4816

European-Finnish (FIN) AF: 0.268 AC: 2830 AN: 10562

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16993 AN: 67972

Other (OTH) AF: 0.285 AC: 600 AN: 2106

Alfa AF: 0.261 Hom.: 3270

Bravo AF: 0.298

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.76
PhyloP100		0.043

Splicing

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

Other links and lift over

dbSNP: rs11124178; hg19: chr2-239964535;