12-96065564-C-A

Variant names:

• chr12-96065564-C-A
• rs759394

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 0.432 in 151,984 control chromosomes in the GnomAD database, including 14,385 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 0.43 (14385 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 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: 0.431 AC: 65494 AN: 151866 Hom.: 14349 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.432 AC: 65584 AN: 151984 Hom.: 14385 Cov.: 32 AF XY: 0.427 AC XY: 31720 AN XY: 74288

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.433

Alfa AF: 0.410 Hom.: 24465

Bravo AF: 0.447

Asia WGS AF: 0.291 AC: 1012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.14
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs759394; hg19: chr12-96459342;