12-97296412-T-C

Variant names:

• chr12-97296412-T-C
• rs2193009

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.194 AC: 8072 AN: 41510

American (AMR) AF: 0.232 AC: 3544 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 619 AN: 3468

East Asian (EAS) AF: 0.0272 AC: 141 AN: 5182

South Asian (SAS) AF: 0.209 AC: 1007 AN: 4824

European-Finnish (FIN) AF: 0.200 AC: 2120 AN: 10598

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14209 AN: 67980

Other (OTH) AF: 0.183 AC: 386 AN: 2112

Alfa AF: 0.201 Hom.: 13451

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
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs2193009; hg19: chr12-97690190;