11-5193183-T-A

Variant names:

• chr11-5193183-T-A
• rs10837540

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 0.518 in 151,702 control chromosomes in the GnomAD database, including 21,068 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 0.52 (21068 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 0 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 = 0.627 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78483 AN: 151584 Hom.: 21041 Cov.: 30

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.518 AC: 78560 AN: 151702 Hom.: 21068 Cov.: 30 AF XY: 0.506 AC XY: 37543 AN XY: 74174

African (AFR) AF: 0.633 AC: 26170 AN: 41334

American (AMR) AF: 0.389 AC: 5927 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1568 AN: 3466

East Asian (EAS) AF: 0.251 AC: 1295 AN: 5162

South Asian (SAS) AF: 0.396 AC: 1898 AN: 4798

European-Finnish (FIN) AF: 0.467 AC: 4897 AN: 10492

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35149 AN: 67914

Other (OTH) AF: 0.505 AC: 1063 AN: 2104

Alfa AF: 0.528 Hom.: 2547

Bravo AF: 0.521

Asia WGS AF: 0.347 AC: 1209 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.33
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10837540; hg19: chr11-5214413;