chr12-132169401-T-A

Position:

• chr12-132169401-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.11 (850 hom., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 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: 0.112 AC: 5578 AN: 49598 Hom.: 849 Cov.: 0

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.0781

Gnomad ASJ AF: 0.0419

Gnomad EAS AF: 0.0373

Gnomad SAS AF: 0.0848

Gnomad FIN AF: 0.0932

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.112 AC: 5580 AN: 49604 Hom.: 850 Cov.: 0 AF XY: 0.106 AC XY: 2590 AN XY: 24482

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.0778

Gnomad4 ASJ AF: 0.0419

Gnomad4 EAS AF: 0.0374

Gnomad4 SAS AF: 0.0858

Gnomad4 FIN AF: 0.0932

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.112

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	4.0
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7133868; hg19: chr12-132653946;