12-94133780-T-G

Position:

• chr12-94133780-T-G

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 0.103 in 142,180 control chromosomes in the GnomAD database, including 781 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 0.10 (781 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.103 AC: 14648 AN: 142064 Hom.: 777 Cov.: 29

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0430

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0791

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.103 AC: 14656 AN: 142180 Hom.: 781 Cov.: 29 AF XY: 0.106 AC XY: 7320 AN XY: 68854

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.0430

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.0791

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0768 Hom.: 671

Bravo AF: 0.102

Asia WGS AF: 0.139 AC: 485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12099972; hg19: chr12-94527556;