rs2882452

Variant names:

• chr2-6059998-T-A
• rs2882452

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.104 in 152,190 control chromosomes in the GnomAD database, including 1,295 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 0.10 (1295 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.17

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.16).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.413 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: 0.104 AC: 15778 AN: 152072 Hom.: 1291 Cov.: 33

Gnomad AFR AF: 0.0869

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0608

Gnomad OTH AF: 0.0988

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

GnomAD4 genome AF: 0.104 AC: 15792 AN: 152190 Hom.: 1295 Cov.: 33 AF XY: 0.113 AC XY: 8429 AN XY: 74410

Gnomad4 AFR AF: 0.0868

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.0608

Gnomad4 OTH AF: 0.0969

Alfa AF: 0.0806 Hom.: 75

Bravo AF: 0.101

Asia WGS AF: 0.292 AC: 1012 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.16
CADD	Benign	20
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2882452; hg19: chr2-6200130;