12-39291731-G-A

Position:

• chr12-39291731-G-A

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 0.0679 in 152,282 control chromosomes in the GnomAD database, including 721 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 0.068 (721 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0679 AC: 10330 AN: 152164 Hom.: 719 Cov.: 32

Gnomad AFR AF: 0.0163

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.0772

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.0557

Gnomad FIN AF: 0.0682

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0543

Gnomad OTH AF: 0.0917

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

GnomAD4 genome AF: 0.0679 AC: 10342 AN: 152282 Hom.: 721 Cov.: 32 AF XY: 0.0710 AC XY: 5289 AN XY: 74468

Gnomad4 AFR AF: 0.0162

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.0772

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.0557

Gnomad4 FIN AF: 0.0682

Gnomad4 NFE AF: 0.0543

Gnomad4 OTH AF: 0.0922

Alfa AF: 0.0680 Hom.: 667

Bravo AF: 0.0796

Asia WGS AF: 0.173 AC: 598 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.3
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4768736; hg19: chr12-39685533;