12-25259195-T-C

Variant names:

• chr12-25259195-T-C
• rs11612828

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 0.317 in 151,928 control chromosomes in the GnomAD database, including 7,814 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 0.32 (7814 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 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: 0.317 AC: 48154 AN: 151810 Hom.: 7796 Cov.: 31

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.317 AC: 48203 AN: 151928 Hom.: 7814 Cov.: 31 AF XY: 0.317 AC XY: 23574 AN XY: 74266

African (AFR) AF: 0.266 AC: 11039 AN: 41426

American (AMR) AF: 0.351 AC: 5358 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1355 AN: 3470

East Asian (EAS) AF: 0.424 AC: 2197 AN: 5176

South Asian (SAS) AF: 0.273 AC: 1315 AN: 4814

European-Finnish (FIN) AF: 0.294 AC: 3088 AN: 10504

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22832 AN: 67948

Other (OTH) AF: 0.323 AC: 683 AN: 2114

Alfa AF: 0.325 Hom.: 1001

Bravo AF: 0.323

Asia WGS AF: 0.347 AC: 1204 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	14
DANN	Benign	0.92
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs11612828; hg19: chr12-25412129; COSMIC: COSV64597909;