11-92024553-C-T

Variant names:

• chr11-92024553-C-T
• rs1793089

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 0.41 in 151,858 control chromosomes in the GnomAD database, including 14,357 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 0.41 (14357 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 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: 0.410 AC: 62157 AN: 151740 Hom.: 14320 Cov.: 31

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.410 AC: 62242 AN: 151858 Hom.: 14357 Cov.: 31 AF XY: 0.402 AC XY: 29804 AN XY: 74228

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.389

Alfa AF: 0.344 Hom.: 5073

Bravo AF: 0.428

Asia WGS AF: 0.244 AC: 846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1793089; hg19: chr11-91757719;