rs12307997

chr12-7702675-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 0.852 in 150,610 control chromosomes in the GnomAD database, including 54,924 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 0.85 (54924 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.886 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: 0.852 AC: 128196 AN: 150490 Hom.: 54896 Cov.: 25

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.854

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.916

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.843

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

GnomAD4 genome AF: 0.852 AC: 128270 AN: 150610 Hom.: 54924 Cov.: 25 AF XY: 0.850 AC XY: 62476 AN XY: 73492

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.854

Gnomad4 EAS AF: 0.845

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.916

Gnomad4 NFE AF: 0.890

Gnomad4 OTH AF: 0.842

Alfa AF: 0.875 Hom.: 7237

Bravo AF: 0.837

Asia WGS AF: 0.878 AC: 3054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	2.9
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12307997; hg19: chr12-7855271;