chr2-108015273-A-G

Variant names:

• chr2-108015273-A-G
• rs10496417

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.553 AC: 22943 AN: 41452

American (AMR) AF: 0.633 AC: 9641 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1974 AN: 3468

East Asian (EAS) AF: 0.827 AC: 4272 AN: 5168

South Asian (SAS) AF: 0.658 AC: 3168 AN: 4818

European-Finnish (FIN) AF: 0.727 AC: 7687 AN: 10578

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41933 AN: 67954

Other (OTH) AF: 0.643 AC: 1356 AN: 2110

Alfa AF: 0.616 Hom.: 88378

Bravo AF: 0.609

Asia WGS AF: 0.721 AC: 2509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	13
DANN	Benign	0.84
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs10496417; hg19: chr2-108631729;