rs759394

Variant names:

• chr12-96065564-C-A
• rs759394

Your query was ambiguous. Multiple possible variants found:

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

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 0.432 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
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.500 AC: 20713 AN: 41436

American (AMR) AF: 0.485 AC: 7413 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1432 AN: 3468

East Asian (EAS) AF: 0.206 AC: 1066 AN: 5168

South Asian (SAS) AF: 0.305 AC: 1470 AN: 4816

European-Finnish (FIN) AF: 0.372 AC: 3919 AN: 10538

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28132 AN: 67960

Other (OTH) AF: 0.433 AC: 914 AN: 2110

Alfa AF: 0.417 Hom.: 56578

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
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs759394; hg19: chr12-96459342;