2-129776708-T-C

Variant names:

• chr2-129776708-T-C
• rs7578253

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 0.41 in 151,902 control chromosomes in the GnomAD database, including 13,449 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 0.41 (13449 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.542 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: 0.410 AC: 62171 AN: 151784 Hom.: 13406 Cov.: 32

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.410 AC: 62265 AN: 151902 Hom.: 13449 Cov.: 32 AF XY: 0.404 AC XY: 29991 AN XY: 74222

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.384

Alfa AF: 0.374 Hom.: 23155

Bravo AF: 0.420

Asia WGS AF: 0.286 AC: 997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.1
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7578253; hg19: chr2-130534281;