12-114129319-A-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 0.639 in 151,992 control chromosomes in the GnomAD database, including 31,978 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 0.64 (31978 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.775 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: 0.639 AC: 97066 AN: 151874 Hom.: 31933 Cov.: 32

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.639 AC: 97169 AN: 151992 Hom.: 31978 Cov.: 32 AF XY: 0.641 AC XY: 47657 AN XY: 74294

Gnomad4 AFR AF: 0.782

Gnomad4 AMR AF: 0.703

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.549

Gnomad4 SAS AF: 0.695

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.637

Alfa AF: 0.583 Hom.: 2751

Bravo AF: 0.656

Asia WGS AF: 0.637 AC: 2213 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.5
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1920586; hg19: chr12-114567124;