rs1798294

chr12-130287208-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 0.131 in 152,176 control chromosomes in the GnomAD database, including 1,629 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 0.13 (1629 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.298 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: 0.131 AC: 19968 AN: 152058 Hom.: 1628 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.0604

Gnomad AMR AF: 0.0998

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0916

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0893

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.131 AC: 19985 AN: 152176 Hom.: 1629 Cov.: 32 AF XY: 0.132 AC XY: 9789 AN XY: 74394

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0916

Gnomad4 NFE AF: 0.0892

Gnomad4 OTH AF: 0.122

Alfa AF: 0.112 Hom.: 228

Bravo AF: 0.137

Asia WGS AF: 0.195 AC: 678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	7.5
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1798294; hg19: chr12-130771753;