12-56045425-A-G

Position:

• chr12-56045425-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 0.145 in 152,086 control chromosomes in the GnomAD database, including 1,869 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 0.15 (1869 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431

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 (SAS) allele frequency at 95% confidence interval = 0.323 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: 0.145 AC: 22072 AN: 151966 Hom.: 1867 Cov.: 31

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.145 AC: 22089 AN: 152086 Hom.: 1869 Cov.: 31 AF XY: 0.151 AC XY: 11210 AN XY: 74344

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.148

Alfa AF: 0.138 Hom.: 3371

Bravo AF: 0.142

Asia WGS AF: 0.310 AC: 1077 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	2.2
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: rs12580100; hg19: chr12-56439209;