2-118693667-G-T

Variant names:

• chr2-118693667-G-T
• rs332735

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 0.835 in 152,252 control chromosomes in the GnomAD database, including 53,888 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 0.84 (53888 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.148
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.835 AC: 127084 AN: 152134 Hom.: 53826 Cov.: 33

Gnomad AFR AF: 0.958

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.835 AC: 127206 AN: 152252 Hom.: 53888 Cov.: 33 AF XY: 0.833 AC XY: 62030 AN XY: 74426

African (AFR) AF: 0.958 AC: 39855 AN: 41582

American (AMR) AF: 0.841 AC: 12861 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3060 AN: 3470

East Asian (EAS) AF: 0.972 AC: 5032 AN: 5176

South Asian (SAS) AF: 0.890 AC: 4295 AN: 4826

European-Finnish (FIN) AF: 0.702 AC: 7430 AN: 10590

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.763 AC: 51874 AN: 67994

Other (OTH) AF: 0.860 AC: 1819 AN: 2116

Alfa AF: 0.807 Hom.: 9532

Bravo AF: 0.853

Asia WGS AF: 0.948 AC: 3295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.39
DANN	Benign	0.60
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs332735; hg19: chr2-119451243;