11-13254782-C-T

Variant names:

• chr11-13254782-C-T
• rs10832008

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 0.155 in 152,044 control chromosomes in the GnomAD database, including 1,940 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 0.15 (1940 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.213 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: 0.155 AC: 23483 AN: 151926 Hom.: 1935 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.155 AC: 23515 AN: 152044 Hom.: 1940 Cov.: 32 AF XY: 0.159 AC XY: 11850 AN XY: 74314

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.153

Alfa AF: 0.143 Hom.: 3297

Bravo AF: 0.152

Asia WGS AF: 0.202 AC: 703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.3
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10832008; hg19: chr11-13276329;