rs11183300

Positions:

• chr12-46042424-C-T

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 0.424 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

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.406

Alfa AF: 0.440 Hom.: 20693

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

Splicing

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

Publications

LitVar

Other links and lift over

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