12-97296412-T-C

Variant names:

• chr12-97296412-T-C
• rs2193009

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 0.199 in 152,162 control chromosomes in the GnomAD database, including 3,057 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 0.20 (3057 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.226 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: 0.199 AC: 30236 AN: 152044 Hom.: 3052 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0271

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.199 AC: 30262 AN: 152162 Hom.: 3057 Cov.: 32 AF XY: 0.197 AC XY: 14689 AN XY: 74396

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.0272

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.183

Alfa AF: 0.199 Hom.: 6405

Bravo AF: 0.199

Asia WGS AF: 0.173 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	5.2
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2193009; hg19: chr12-97690190;