rs486098

Variant names:

• chr12-279491-C-T
• rs486098

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 0.244 in 152,124 control chromosomes in the GnomAD database, including 4,691 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 0.24 (4691 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.296 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: 0.244 AC: 37071 AN: 152006 Hom.: 4682 Cov.: 33

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.244 AC: 37102 AN: 152124 Hom.: 4691 Cov.: 33 AF XY: 0.246 AC XY: 18303 AN XY: 74354

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.216

Alfa AF: 0.246 Hom.: 5050

Bravo AF: 0.232

Asia WGS AF: 0.257 AC: 893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.85
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs486098; hg19: chr12-388657;