12-28796392-G-T

Variant names:

• chr12-28796392-G-T
• rs309045

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 0.467 in 152,052 control chromosomes in the GnomAD database, including 18,153 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 0.47 (18153 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392

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 (EAS) allele frequency at 95% confidence interval = 0.846 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: 0.467 AC: 70988 AN: 151934 Hom.: 18124 Cov.: 33

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.467 AC: 71061 AN: 152052 Hom.: 18153 Cov.: 33 AF XY: 0.477 AC XY: 35457 AN XY: 74304

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.867

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.599

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.461

Alfa AF: 0.505 Hom.: 8894

Bravo AF: 0.465

Asia WGS AF: 0.654 AC: 2275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.54
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs309045; hg19: chr12-28949325;