12-13284616-G-C

Variant names:

• chr12-13284616-G-C
• rs4763333

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 0.424 in 152,024 control chromosomes in the GnomAD database, including 14,848 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 0.42 (14848 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 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: 0.424 AC: 64396 AN: 151904 Hom.: 14831 Cov.: 32

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.424 AC: 64455 AN: 152024 Hom.: 14848 Cov.: 32 AF XY: 0.414 AC XY: 30767 AN XY: 74318

Gnomad4 AFR AF: 0.605

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.379

Alfa AF: 0.424 Hom.: 1786

Bravo AF: 0.424

Asia WGS AF: 0.306 AC: 1069 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	0.30
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4763333; hg19: chr12-13437550;