rs10837540

Variant names:

• chr11-5193183-T-A
• rs10837540

Your query was ambiguous. Multiple possible variants found:

• chr11-5193183-T-A
• chr11-5193183-T-G

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 0.518 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

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 = 0.627 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: 0.518 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

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.505

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10837540; hg19: chr11-5214413;