rs12913946

Positions:

• chr15-78417595-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;