2-118718424-C-A

Variant names:

• chr2-118718424-C-A
• rs332090

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 0.775 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.796 AC: 33010 AN: 41478

American (AMR) AF: 0.780 AC: 11929 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2487 AN: 3470

East Asian (EAS) AF: 0.863 AC: 4454 AN: 5160

South Asian (SAS) AF: 0.588 AC: 2825 AN: 4802

European-Finnish (FIN) AF: 0.725 AC: 7657 AN: 10568

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.782 AC: 53160 AN: 67982

Other (OTH) AF: 0.779 AC: 1647 AN: 2114

Alfa AF: 0.779 Hom.: 7745

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
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs332090; hg19: chr2-119476000;