rs12913946

Variant names:

• chr15-78417595-T-C
• rs12913946

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 0.808 in 152,242 control chromosomes in the GnomAD database, including 50,074 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 0.81 (50074 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.901 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: 0.808 AC: 122944 AN: 152124 Hom.: 50002 Cov.: 34

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.801

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.808 AC: 123076 AN: 152242 Hom.: 50074 Cov.: 34 AF XY: 0.808 AC XY: 60104 AN XY: 74424

Gnomad4 AFR AF: 0.909

Gnomad4 AMR AF: 0.808

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.802

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.780

Gnomad4 NFE AF: 0.764

Gnomad4 OTH AF: 0.786

Alfa AF: 0.769 Hom.: 28875

Bravo AF: 0.817

Asia WGS AF: 0.788 AC: 2737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12913946; hg19: chr15-78709937;