11-92940662-C-T

Variant names:

• chr11-92940662-C-T
• rs1387153

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 0.317 in 151,984 control chromosomes in the GnomAD database, including 7,801 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 0.32 (7801 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.429 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: 0.317 AC: 48157 AN: 151864 Hom.: 7801 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.317 AC: 48184 AN: 151984 Hom.: 7801 Cov.: 32 AF XY: 0.319 AC XY: 23711 AN XY: 74272

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.301

Alfa AF: 0.291 Hom.: 15107

Bravo AF: 0.308

Asia WGS AF: 0.354 AC: 1229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.4
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1387153; hg19: chr11-92673828;