rs12899131

Variant names:

• chr15-78434543-A-G
• rs12899131

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.365 in 151,908 control chromosomes in the GnomAD database, including 10,872 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 0.37 (10872 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 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: 0.365 AC: 55465 AN: 151790 Hom.: 10870 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.365 AC: 55485 AN: 151908 Hom.: 10872 Cov.: 31 AF XY: 0.368 AC XY: 27288 AN XY: 74238

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.372

Alfa AF: 0.412 Hom.: 7057

Bravo AF: 0.354

Asia WGS AF: 0.406 AC: 1411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	14
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12899131; hg19: chr15-78726885;