rs11055792

chr12-14138366-C-T

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 0.39 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.364

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.377

Alfa AF: 0.432 Hom.: 16499

Bravo AF: 0.368

Asia WGS AF: 0.378 AC: 1309 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.33
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11055792; hg19: chr12-14291300;