12-98424524-C-T

Variant names:

• chr12-98424524-C-T
• rs1468832

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 0.106 in 152,194 control chromosomes in the GnomAD database, including 1,213 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 0.11 (1213 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 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: 0.106 AC: 16173 AN: 152076 Hom.: 1213 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.0726

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0296

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.0790

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0616

Gnomad OTH AF: 0.0894

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

GnomAD4 genome AF: 0.106 AC: 16188 AN: 152194 Hom.: 1213 Cov.: 32 AF XY: 0.104 AC XY: 7776 AN XY: 74430

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.0724

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.0299

Gnomad4 SAS AF: 0.0172

Gnomad4 FIN AF: 0.0790

Gnomad4 NFE AF: 0.0616

Gnomad4 OTH AF: 0.0885

Alfa AF: 0.0670 Hom.: 877

Bravo AF: 0.114

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1468832; hg19: chr12-98818302;