2-128332535-C-T

Variant names:

• chr2-128332535-C-T
• rs11890277

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;