12-107201789-C-T

Variant names:

• chr12-107201789-C-T
• rs12422243

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 0.176 in 152,110 control chromosomes in the GnomAD database, including 3,020 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 0.18 (3020 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.268

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.236 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: 0.176 AC: 26721 AN: 151992 Hom.: 3011 Cov.: 32

Gnomad AFR AF: 0.0483

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.176 AC: 26749 AN: 152110 Hom.: 3020 Cov.: 32 AF XY: 0.180 AC XY: 13354 AN XY: 74340

Gnomad4 AFR AF: 0.0482

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.175

Alfa AF: 0.207 Hom.: 1410

Bravo AF: 0.167

Asia WGS AF: 0.172 AC: 597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.3
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12422243; hg19: chr12-107595567;