2-128332535-C-T

Position:

• chr2-128332535-C-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 0.127 in 152,110 control chromosomes in the GnomAD database, including 1,345 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 0.13 (1345 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.195 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: 0.127 AC: 19350 AN: 151992 Hom.: 1341 Cov.: 33

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.127 AC: 19365 AN: 152110 Hom.: 1345 Cov.: 33 AF XY: 0.132 AC XY: 9808 AN XY: 74354

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.133

Alfa AF: 0.110 Hom.: 2169

Bravo AF: 0.130

Asia WGS AF: 0.210 AC: 729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.91
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11890277; hg19: chr2-129090109;