rs11113153

Variant names:

• chr12-106987992-C-T
• rs11113153

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 0.128 in 151,102 control chromosomes in the GnomAD database, including 1,603 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 (1603 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.702
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 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: 0.128 AC: 19357 AN: 150992 Hom.: 1600 Cov.: 32

Gnomad AFR AF: 0.0302

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.0671

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.128 AC: 19356 AN: 151102 Hom.: 1603 Cov.: 32 AF XY: 0.130 AC XY: 9625 AN XY: 73792

African (AFR) AF: 0.0301 AC: 1243 AN: 41330

American (AMR) AF: 0.133 AC: 1993 AN: 14930

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 700 AN: 3464

East Asian (EAS) AF: 0.296 AC: 1524 AN: 5144

South Asian (SAS) AF: 0.0678 AC: 319 AN: 4704

European-Finnish (FIN) AF: 0.188 AC: 1980 AN: 10506

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11076 AN: 67714

Other (OTH) AF: 0.144 AC: 304 AN: 2106

Alfa AF: 0.143 Hom.: 2718

Bravo AF: 0.124

Asia WGS AF: 0.170 AC: 591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.9
DANN	Benign	0.46
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs11113153; hg19: chr12-107381770;