rs12307997

Variant names:

• chr12-7702675-G-A
• rs12307997

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.812 AC: 33383 AN: 41130

American (AMR) AF: 0.731 AC: 11079 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.854 AC: 2953 AN: 3456

East Asian (EAS) AF: 0.845 AC: 4103 AN: 4858

South Asian (SAS) AF: 0.909 AC: 4276 AN: 4706

European-Finnish (FIN) AF: 0.916 AC: 9509 AN: 10386

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.890 AC: 60202 AN: 67614

Other (OTH) AF: 0.842 AC: 1771 AN: 2104

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
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs12307997; hg19: chr12-7855271;