chr12-121039713-G-A

Variant names:

• chr12-121039713-G-A
• rs12315068

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 0.133 in 151,214 control chromosomes in the GnomAD database, including 1,580 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 0.13 (1580 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20077 AN: 151098 Hom.: 1575 Cov.: 26

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.0891

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0907

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.133 AC: 20115 AN: 151214 Hom.: 1580 Cov.: 26 AF XY: 0.136 AC XY: 10040 AN XY: 73824

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.0891

Gnomad4 NFE AF: 0.0907

Gnomad4 OTH AF: 0.130

Alfa AF: 0.103 Hom.: 119

Bravo AF: 0.141

Asia WGS AF: 0.232 AC: 806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12315068; hg19: chr12-121477516;