rs332090

Variant names:

• chr2-118718424-C-A
• rs332090

Your query was ambiguous. Multiple possible variants found:

• chr2-118718424-C-A
• chr2-118718424-C-G
• chr2-118718424-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 0.775 in 152,070 control chromosomes in the GnomAD database, including 45,872 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 (45872 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754

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 (EAS) allele frequency at 95% confidence interval = 0.842 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: 0.775 AC: 117817 AN: 151956 Hom.: 45833 Cov.: 31

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.775 AC: 117902 AN: 152070 Hom.: 45872 Cov.: 31 AF XY: 0.771 AC XY: 57302 AN XY: 74334

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.780

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.863

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.782

Gnomad4 OTH AF: 0.779

Alfa AF: 0.778 Hom.: 7498

Bravo AF: 0.783

Asia WGS AF: 0.740 AC: 2568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.16
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs332090; hg19: chr2-119476000;