12-121041852-T-C

Position:

• chr12-121041852-T-C

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 0.297 in 147,228 control chromosomes in the GnomAD database, including 7,042 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 0.30 (7042 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

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 = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.297 AC: 43724 AN: 147120 Hom.: 7041 Cov.: 24

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.526

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.297 AC: 43725 AN: 147228 Hom.: 7042 Cov.: 24 AF XY: 0.304 AC XY: 21704 AN XY: 71392

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.328

Alfa AF: 0.298 Hom.: 884

Bravo AF: 0.282

Asia WGS AF: 0.434 AC: 1506 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.9
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2859398; hg19: chr12-121479655;