rs10500786

Variant names:

• chr11-13562237-G-A
• rs10500786

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 0.373 in 152,050 control chromosomes in the GnomAD database, including 12,107 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 0.37 (12107 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.48 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: 0.374 AC: 56770 AN: 151932 Hom.: 12111 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.373 AC: 56773 AN: 152050 Hom.: 12107 Cov.: 32 AF XY: 0.372 AC XY: 27630 AN XY: 74330

African (AFR) AF: 0.187 AC: 7773 AN: 41478

American (AMR) AF: 0.361 AC: 5514 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1782 AN: 3466

East Asian (EAS) AF: 0.170 AC: 881 AN: 5176

South Asian (SAS) AF: 0.272 AC: 1309 AN: 4818

European-Finnish (FIN) AF: 0.495 AC: 5235 AN: 10572

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.485 AC: 32938 AN: 67966

Other (OTH) AF: 0.375 AC: 792 AN: 2114

Alfa AF: 0.440 Hom.: 50040

Bravo AF: 0.354

Asia WGS AF: 0.226 AC: 788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.28
DANN	Benign	0.33
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10500786; hg19: chr11-13583784;