rs11183940

Variant names:

• chr12-38457840-A-G
• rs11183940

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 0.293 in 151,700 control chromosomes in the GnomAD database, including 8,437 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 (8437 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.415 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: 0.293 AC: 44425 AN: 151582 Hom.: 8435 Cov.: 32

Gnomad AFR AF: 0.0868

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.0395

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.293 AC: 44419 AN: 151700 Hom.: 8437 Cov.: 32 AF XY: 0.292 AC XY: 21605 AN XY: 74098

Gnomad4 AFR AF: 0.0865

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.0394

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.277

Alfa AF: 0.378 Hom.: 5416

Bravo AF: 0.271

Asia WGS AF: 0.133 AC: 463 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	2.2
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11183940; hg19: chr12-38851642; COSMIC: COSV63288192;