rs11124178

Positions:

• chr2-239042839-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.0424

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.285

Alfa AF: 0.261 Hom.: 1535

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11124178; hg19: chr2-239964535;