rs12913838

Variant names:

• chr15-87813028-T-C
• rs12913838

Your query was ambiguous. Multiple possible variants found:

• chr15-87813028-T-C
• chr15-87813028-T-G

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 0.293 in 151,938 control chromosomes in the GnomAD database, including 7,223 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 0.29 (7223 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 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: 0.294 AC: 44564 AN: 151822 Hom.: 7225 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.293 AC: 44560 AN: 151938 Hom.: 7223 Cov.: 33 AF XY: 0.295 AC XY: 21894 AN XY: 74238

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.314

Alfa AF: 0.193 Hom.: 474

Bravo AF: 0.291

Asia WGS AF: 0.363 AC: 1260 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.7
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12913838; hg19: chr15-88356259;