12-114508483-A-G

Position:

• chr12-114508483-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 0.219 in 152,120 control chromosomes in the GnomAD database, including 5,402 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 0.22 (5402 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.968

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.434 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: 0.219 AC: 33239 AN: 152002 Hom.: 5377 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0744

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.219 AC: 33314 AN: 152120 Hom.: 5402 Cov.: 32 AF XY: 0.216 AC XY: 16077 AN XY: 74372

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0744

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.192

Alfa AF: 0.134 Hom.: 3152

Bravo AF: 0.243

Asia WGS AF: 0.264 AC: 919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.13
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7967827; hg19: chr12-114946288;