12-29383451-A-T

Variant names:

• chr12-29383451-A-T
• rs10743657

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.657 AC: 27230 AN: 41430

American (AMR) AF: 0.689 AC: 10526 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2243 AN: 3470

East Asian (EAS) AF: 0.580 AC: 3001 AN: 5170

South Asian (SAS) AF: 0.590 AC: 2848 AN: 4824

European-Finnish (FIN) AF: 0.505 AC: 5336 AN: 10572

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38110 AN: 67924

Other (OTH) AF: 0.623 AC: 1314 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.3
DANN	Benign	0.68
PhyloP100		0.085

Splicing

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

Other links and lift over

dbSNP: rs10743657; hg19: chr12-29536384;