2-130261616-T-C

Variant names:

• chr2-130261616-T-C
• rs938869

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 0.465 in 152,050 control chromosomes in the GnomAD database, including 17,297 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 0.46 (17297 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.686

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.539 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: 0.465 AC: 70655 AN: 151932 Hom.: 17293 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.465 AC: 70671 AN: 152050 Hom.: 17297 Cov.: 32 AF XY: 0.467 AC XY: 34707 AN XY: 74310

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.460

Alfa AF: 0.522 Hom.: 11192

Bravo AF: 0.457

Asia WGS AF: 0.440 AC: 1531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	5.6
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs938869; hg19: chr2-131019189;