rs11183300

Variant names:

• chr12-46042424-C-T
• rs11183300

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 0.424 in 151,888 control chromosomes in the GnomAD database, including 13,892 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 (13892 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.55 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: 0.424 AC: 64328 AN: 151770 Hom.: 13883 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.424 AC: 64362 AN: 151888 Hom.: 13892 Cov.: 32 AF XY: 0.431 AC XY: 31966 AN XY: 74242

African (AFR) AF: 0.337 AC: 13953 AN: 41408

American (AMR) AF: 0.426 AC: 6492 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1773 AN: 3470

East Asian (EAS) AF: 0.560 AC: 2890 AN: 5160

South Asian (SAS) AF: 0.568 AC: 2737 AN: 4820

European-Finnish (FIN) AF: 0.479 AC: 5043 AN: 10524

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.442 AC: 30029 AN: 67936

Other (OTH) AF: 0.406 AC: 859 AN: 2116

Alfa AF: 0.433 Hom.: 48741

Bravo AF: 0.414

Asia WGS AF: 0.503 AC: 1746 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.4
DANN	Benign	0.64
PhyloP100		0.042

Splicing

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

Other links and lift over

dbSNP: rs11183300; hg19: chr12-46436207; COSMIC: COSV56567360;