chr11-92024553-C-T

Variant names:

• chr11-92024553-C-T
• rs1793089

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.633 AC: 26208 AN: 41418

American (AMR) AF: 0.364 AC: 5554 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1192 AN: 3464

East Asian (EAS) AF: 0.234 AC: 1204 AN: 5156

South Asian (SAS) AF: 0.198 AC: 953 AN: 4814

European-Finnish (FIN) AF: 0.323 AC: 3404 AN: 10548

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.333 AC: 22596 AN: 67886

Other (OTH) AF: 0.389 AC: 821 AN: 2108

Alfa AF: 0.352 Hom.: 7285

Bravo AF: 0.428

Asia WGS AF: 0.244 AC: 846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.57
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1793089; hg19: chr11-91757719;