2-108015273-A-G

Variant names:

• chr2-108015273-A-G
• rs10496417

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 0.616 in 151,992 control chromosomes in the GnomAD database, including 29,084 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 0.62 (29084 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 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: 0.616 AC: 93507 AN: 151872 Hom.: 29051 Cov.: 32

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.616 AC: 93587 AN: 151992 Hom.: 29084 Cov.: 32 AF XY: 0.623 AC XY: 46285 AN XY: 74278

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.727

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.643

Alfa AF: 0.619 Hom.: 59141

Bravo AF: 0.609

Asia WGS AF: 0.721 AC: 2509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	13
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496417; hg19: chr2-108631729;