rs2090602

Variant names:

• chr11-45831095-T-C
• rs2090602

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 0.777 in 152,042 control chromosomes in the GnomAD database, including 47,331 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 0.78 (47331 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.873 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: 0.777 AC: 118077 AN: 151924 Hom.: 47311 Cov.: 31

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.812

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.777 AC: 118146 AN: 152042 Hom.: 47331 Cov.: 31 AF XY: 0.775 AC XY: 57646 AN XY: 74348

African (AFR) AF: 0.626 AC: 25932 AN: 41428

American (AMR) AF: 0.761 AC: 11625 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.891 AC: 3093 AN: 3470

East Asian (EAS) AF: 0.373 AC: 1923 AN: 5158

South Asian (SAS) AF: 0.790 AC: 3810 AN: 4820

European-Finnish (FIN) AF: 0.885 AC: 9366 AN: 10578

Middle Eastern (MID) AF: 0.808 AC: 236 AN: 292

European-Non Finnish (NFE) AF: 0.879 AC: 59738 AN: 67994

Other (OTH) AF: 0.781 AC: 1647 AN: 2110

Alfa AF: 0.844 Hom.: 91668

Bravo AF: 0.756

Asia WGS AF: 0.673 AC: 2343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.50
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs2090602; hg19: chr11-45852646;