2-133886738-G-T

Position:

• chr2-133886738-G-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 0.199 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;