rs3025090

Variant names:

• chr11-102844152-G-A
• rs3025090

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 0.0784 in 152,188 control chromosomes in the GnomAD database, including 516 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 0.078 (516 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0902 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: 0.0784 AC: 11922 AN: 152070 Hom.: 515 Cov.: 33

Gnomad AFR AF: 0.0695

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.0680

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0612

Gnomad FIN AF: 0.0585

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0922

Gnomad OTH AF: 0.0807

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

GnomAD4 genome AF: 0.0784 AC: 11928 AN: 152188 Hom.: 516 Cov.: 33 AF XY: 0.0771 AC XY: 5733 AN XY: 74388

African (AFR) AF: 0.0696 AC: 2888 AN: 41516

American (AMR) AF: 0.0679 AC: 1038 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 461 AN: 3470

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5188

South Asian (SAS) AF: 0.0616 AC: 297 AN: 4818

European-Finnish (FIN) AF: 0.0585 AC: 619 AN: 10584

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.0921 AC: 6266 AN: 68000

Other (OTH) AF: 0.0799 AC: 169 AN: 2116

Alfa AF: 0.0819 Hom.: 73

Bravo AF: 0.0783

Asia WGS AF: 0.0400 AC: 138 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	0.49
DANN	Benign	0.42
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs3025090; hg19: chr11-102714883;