rs938869

chr2-130261616-T-Cchr2-130261616-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;