chr11-13552067-C-T

Variant names:

• chr11-13552067-C-T
• rs10500783

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 0.13 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0662 AC: 2750 AN: 41524

American (AMR) AF: 0.118 AC: 1803 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 641 AN: 3470

East Asian (EAS) AF: 0.131 AC: 676 AN: 5178

South Asian (SAS) AF: 0.319 AC: 1536 AN: 4816

European-Finnish (FIN) AF: 0.134 AC: 1423 AN: 10590

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10521 AN: 68018

Other (OTH) AF: 0.149 AC: 315 AN: 2108

Alfa AF: 0.134 Hom.: 285

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
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs10500783; hg19: chr11-13573614;