12-128251977-C-T

Variant names:

• chr12-128251977-C-T
• rs12297524

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 0.319 in 151,984 control chromosomes in the GnomAD database, including 8,130 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 (8130 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.371 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: 0.319 AC: 48405 AN: 151866 Hom.: 8124 Cov.: 33

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.319 AC: 48435 AN: 151984 Hom.: 8130 Cov.: 33 AF XY: 0.317 AC XY: 23515 AN XY: 74290

African (AFR) AF: 0.220 AC: 9112 AN: 41434

American (AMR) AF: 0.379 AC: 5783 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1028 AN: 3472

East Asian (EAS) AF: 0.325 AC: 1682 AN: 5168

South Asian (SAS) AF: 0.344 AC: 1659 AN: 4816

European-Finnish (FIN) AF: 0.301 AC: 3179 AN: 10552

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24952 AN: 67966

Other (OTH) AF: 0.314 AC: 663 AN: 2112

Alfa AF: 0.344 Hom.: 13370

Bravo AF: 0.322

Asia WGS AF: 0.303 AC: 1050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.9
DANN	Benign	0.63
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs12297524; hg19: chr12-128736522;