11-13230267-C-T

Variant names:

• chr11-13230267-C-T
• rs10832001

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 0.191 in 152,140 control chromosomes in the GnomAD database, including 3,246 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 0.19 (3246 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.254 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: 0.191 AC: 29031 AN: 152022 Hom.: 3241 Cov.: 33

Gnomad AFR AF: 0.0877

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.191 AC: 29056 AN: 152140 Hom.: 3246 Cov.: 33 AF XY: 0.196 AC XY: 14597 AN XY: 74346

African (AFR) AF: 0.0877 AC: 3643 AN: 41532

American (AMR) AF: 0.261 AC: 3991 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 761 AN: 3472

East Asian (EAS) AF: 0.146 AC: 757 AN: 5170

South Asian (SAS) AF: 0.206 AC: 993 AN: 4820

European-Finnish (FIN) AF: 0.311 AC: 3284 AN: 10574

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14938 AN: 67970

Other (OTH) AF: 0.180 AC: 381 AN: 2114

Alfa AF: 0.179 Hom.: 919

Bravo AF: 0.185

Asia WGS AF: 0.181 AC: 629 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.4
DANN	Benign	0.59
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs10832001; hg19: chr11-13251814;