rs759394

Positions:

• chr12-96065564-C-A
• chr12-96065564-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;