rs2902376

Variant names:

• chr2-82564281-A-G
• rs2902376

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 0.357 in 152,066 control chromosomes in the GnomAD database, including 11,716 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 0.36 (11716 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 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: 0.357 AC: 54249 AN: 151950 Hom.: 11684 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0429

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.357 AC: 54320 AN: 152066 Hom.: 11716 Cov.: 32 AF XY: 0.350 AC XY: 26017 AN XY: 74338

Gnomad4 AFR AF: 0.600

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.0428

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.316

Alfa AF: 0.307 Hom.: 4050

Bravo AF: 0.368

Asia WGS AF: 0.143 AC: 498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2902376; hg19: chr2-82791405;