11-92947847-C-T

Position:

• chr11-92947847-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 0.328 in 151,928 control chromosomes in the GnomAD database, including 8,441 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 0.33 (8441 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 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: 0.328 AC: 49838 AN: 151808 Hom.: 8438 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.328 AC: 49882 AN: 151928 Hom.: 8441 Cov.: 32 AF XY: 0.330 AC XY: 24533 AN XY: 74254

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.314

Alfa AF: 0.298 Hom.: 4689

Bravo AF: 0.321

Asia WGS AF: 0.358 AC: 1243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10830956; hg19: chr11-92681013;