12-29383451-A-T

Position:

• chr12-29383451-A-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 0.602 in 151,986 control chromosomes in the GnomAD database, including 27,822 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 0.60 (27822 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.678 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: 0.602 AC: 91402 AN: 151868 Hom.: 27790 Cov.: 32

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.602 AC: 91483 AN: 151986 Hom.: 27822 Cov.: 32 AF XY: 0.603 AC XY: 44828 AN XY: 74294

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.623

Alfa AF: 0.577 Hom.: 3166

Bravo AF: 0.621

Asia WGS AF: 0.596 AC: 2070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.3
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10743657; hg19: chr12-29536384;