rs12899425

Variant names:

• chr15-78434494-G-A
• rs12899425

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 0.213 in 151,918 control chromosomes in the GnomAD database, including 4,049 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 0.21 (4049 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.568
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 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: 0.213 AC: 32397 AN: 151800 Hom.: 4046 Cov.: 32

Gnomad AFR AF: 0.0836

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.213 AC: 32382 AN: 151918 Hom.: 4049 Cov.: 32 AF XY: 0.215 AC XY: 16002 AN XY: 74260

African (AFR) AF: 0.0834 AC: 3454 AN: 41412

American (AMR) AF: 0.216 AC: 3299 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 686 AN: 3464

East Asian (EAS) AF: 0.324 AC: 1674 AN: 5162

South Asian (SAS) AF: 0.239 AC: 1152 AN: 4820

European-Finnish (FIN) AF: 0.269 AC: 2835 AN: 10524

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18506 AN: 67964

Other (OTH) AF: 0.208 AC: 439 AN: 2108

Alfa AF: 0.225 Hom.: 898

Bravo AF: 0.206

Asia WGS AF: 0.227 AC: 792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.89
DANN	Benign	0.48
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs12899425; hg19: chr15-78726836;