rs12913838

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;