rs11523890

chr11-92946612-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 0.37 in 151,930 control chromosomes in the GnomAD database, including 10,550 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 0.37 (10550 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.429 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: 0.369 AC: 56094 AN: 151812 Hom.: 10546 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.370 AC: 56140 AN: 151930 Hom.: 10550 Cov.: 32 AF XY: 0.370 AC XY: 27482 AN XY: 74232

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.373

Alfa AF: 0.350 Hom.: 1309

Bravo AF: 0.361

Asia WGS AF: 0.364 AC: 1265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.0
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11523890; hg19: chr11-92679778;