rs12817159

Variant names:

• chr12-87295629-G-A
• rs12817159

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 0.228 in 148,914 control chromosomes in the GnomAD database, including 4,232 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 0.23 (4232 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 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: 0.228 AC: 33933 AN: 148810 Hom.: 4224 Cov.: 30

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.228 AC: 33963 AN: 148914 Hom.: 4232 Cov.: 30 AF XY: 0.235 AC XY: 17088 AN XY: 72734

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.221

Alfa AF: 0.211 Hom.: 437

Bravo AF: 0.214

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.95
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12817159; hg19: chr12-87689406;