2-133886738-G-T

Variant names:

• chr2-133886738-G-T
• rs13429789

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 0.199 in 152,026 control chromosomes in the GnomAD database, including 3,087 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 0.20 (3087 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.722

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.242 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: 0.199 AC: 30242 AN: 151908 Hom.: 3085 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.199 AC: 30272 AN: 152026 Hom.: 3087 Cov.: 32 AF XY: 0.203 AC XY: 15114 AN XY: 74296

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.215

Alfa AF: 0.190 Hom.: 2099

Bravo AF: 0.200

Asia WGS AF: 0.252 AC: 875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.55
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13429789; hg19: chr2-134644309;