12-94133780-T-G

Variant names:

• chr12-94133780-T-G
• rs12099972

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;