rs10500783

Positions:

• chr11-13552067-C-T

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 0.13 in 152,184 control chromosomes in the GnomAD database, including 1,514 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 0.13 (1514 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.306 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: 0.130 AC: 19780 AN: 152066 Hom.: 1510 Cov.: 33

Gnomad AFR AF: 0.0664

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.130 AC: 19790 AN: 152184 Hom.: 1514 Cov.: 33 AF XY: 0.134 AC XY: 9939 AN XY: 74386

Gnomad4 AFR AF: 0.0662

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.149

Alfa AF: 0.136 Hom.: 284

Bravo AF: 0.121

Asia WGS AF: 0.220 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.90
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500783; hg19: chr11-13573614;