rs332090

chr2-118718424-C-Achr2-118718424-C-Gchr2-118718424-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;