rs12315068

Variant names:

• chr12-121039713-G-A
• rs12315068

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 0.133 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.192 AC: 7889 AN: 41174

American (AMR) AF: 0.132 AC: 2004 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 392 AN: 3458

East Asian (EAS) AF: 0.280 AC: 1427 AN: 5094

South Asian (SAS) AF: 0.175 AC: 833 AN: 4770

European-Finnish (FIN) AF: 0.0891 AC: 932 AN: 10462

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0907 AC: 6150 AN: 67800

Other (OTH) AF: 0.130 AC: 270 AN: 2082

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
PhyloP100		-0.84
PromoterAI		0.0068	Neutral

Splicing

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

Other links and lift over

dbSNP: rs12315068; hg19: chr12-121477516;