2-118693667-G-T

Variant names:

• chr2-118693667-G-T
• rs332735

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 0.835 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.835 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

Gnomad4 AFR AF: 0.958

Gnomad4 AMR AF: 0.841

Gnomad4 ASJ AF: 0.882

Gnomad4 EAS AF: 0.972

Gnomad4 SAS AF: 0.890

Gnomad4 FIN AF: 0.702

Gnomad4 NFE AF: 0.763

Gnomad4 OTH AF: 0.860

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs332735; hg19: chr2-119451243;