rs10837540

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;