rs12946942

Variant names:

• chr17-71240857-G-T
• rs12946942

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 0.0785 in 152,114 control chromosomes in the GnomAD database, including 713 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 0.079 (713 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.243 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: 0.0786 AC: 11943 AN: 151996 Hom.: 713 Cov.: 32

Gnomad AFR AF: 0.0167

Gnomad AMI AF: 0.0640

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.0850

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.0836

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0738

Gnomad OTH AF: 0.0839

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

GnomAD4 genome AF: 0.0785 AC: 11946 AN: 152114 Hom.: 713 Cov.: 32 AF XY: 0.0839 AC XY: 6236 AN XY: 74360

Gnomad4 AFR AF: 0.0167

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.0850

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.0833

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.0739

Gnomad4 OTH AF: 0.0844

Alfa AF: 0.0819 Hom.: 945

Bravo AF: 0.0811

Asia WGS AF: 0.146 AC: 506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12946942; hg19: chr17-69236998;