rs12366192

Variant names:

• chr11-42283513-T-C
• rs12366192

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 0.128 in 152,134 control chromosomes in the GnomAD database, including 1,327 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 0.13 (1327 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.173 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: 0.127 AC: 19377 AN: 152016 Hom.: 1322 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.0791

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.128 AC: 19404 AN: 152134 Hom.: 1327 Cov.: 32 AF XY: 0.127 AC XY: 9482 AN XY: 74388

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.0791

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.136

Alfa AF: 0.120 Hom.: 625

Bravo AF: 0.132

Asia WGS AF: 0.182 AC: 635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.3
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12366192; hg19: chr11-42305063;