rs12946510

Variant names:

• chr17-39756124-C-T
• rs12946510

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 0.372 in 152,082 control chromosomes in the GnomAD database, including 11,648 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 (11648 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 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: 0.372 AC: 56536 AN: 151964 Hom.: 11644 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.372 AC: 56551 AN: 152082 Hom.: 11648 Cov.: 32 AF XY: 0.375 AC XY: 27859 AN XY: 74350

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.357

Alfa AF: 0.388 Hom.: 2632

Bravo AF: 0.347

Asia WGS AF: 0.371 AC: 1288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	20
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12946510; hg19: chr17-37912377;