12-94689566-C-T

Position:

• chr12-94689566-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 0.461 in 151,904 control chromosomes in the GnomAD database, including 16,308 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 0.46 (16308 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 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: 0.461 AC: 70001 AN: 151782 Hom.: 16288 Cov.: 31

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.461 AC: 70056 AN: 151904 Hom.: 16308 Cov.: 31 AF XY: 0.458 AC XY: 33994 AN XY: 74218

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.451

Alfa AF: 0.476 Hom.: 4969

Bravo AF: 0.454

Asia WGS AF: 0.375 AC: 1306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	12
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7966485; hg19: chr12-95083342;