rs11055792

Variant names:

• chr12-14138366-C-T
• rs11055792

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 0.39 in 146,706 control chromosomes in the GnomAD database, including 12,470 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 0.39 (12470 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.390 AC: 57148 AN: 146594 Hom.: 12462 Cov.: 31

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.390 AC: 57154 AN: 146706 Hom.: 12470 Cov.: 31 AF XY: 0.397 AC XY: 28411 AN XY: 71552

African (AFR) AF: 0.150 AC: 5981 AN: 39828

American (AMR) AF: 0.567 AC: 8519 AN: 15032

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1616 AN: 3434

East Asian (EAS) AF: 0.364 AC: 1558 AN: 4278

South Asian (SAS) AF: 0.468 AC: 2192 AN: 4688

European-Finnish (FIN) AF: 0.540 AC: 5393 AN: 9988

Middle Eastern (MID) AF: 0.371 AC: 106 AN: 286

European-Non Finnish (NFE) AF: 0.461 AC: 30526 AN: 66266

Other (OTH) AF: 0.377 AC: 766 AN: 2034

Alfa AF: 0.426 Hom.: 20183

Bravo AF: 0.368

Asia WGS AF: 0.378 AC: 1309 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.34
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs11055792; hg19: chr12-14291300;