chr12-38457840-A-G

Variant names:

• chr12-38457840-A-G
• rs11183940

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 0.293 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
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.0865 AC: 3589 AN: 41470

American (AMR) AF: 0.268 AC: 4074 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1000 AN: 3460

East Asian (EAS) AF: 0.0394 AC: 203 AN: 5154

South Asian (SAS) AF: 0.240 AC: 1155 AN: 4822

European-Finnish (FIN) AF: 0.476 AC: 5005 AN: 10524

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28436 AN: 67786

Other (OTH) AF: 0.277 AC: 581 AN: 2098

Alfa AF: 0.378 Hom.: 6092

Bravo AF: 0.271

Asia WGS AF: 0.133 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.57
PhyloP100		0.20

Splicing

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

Other links and lift over

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