rs12366192

Positions:

• chr11-42283513-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;