12-121041852-T-C

Variant names:

• chr12-121041852-T-C
• rs2859398

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 0.297 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.164 AC: 6480 AN: 39584

American (AMR) AF: 0.321 AC: 4686 AN: 14610

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1546 AN: 3450

East Asian (EAS) AF: 0.462 AC: 2287 AN: 4948

South Asian (SAS) AF: 0.487 AC: 2261 AN: 4644

European-Finnish (FIN) AF: 0.344 AC: 3277 AN: 9520

Middle Eastern (MID) AF: 0.521 AC: 150 AN: 288

European-Non Finnish (NFE) AF: 0.327 AC: 22032 AN: 67282

Other (OTH) AF: 0.328 AC: 660 AN: 2010

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.9
DANN	Benign	0.44
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2859398; hg19: chr12-121479655;