rs17819128

Variant names:

• chr12-12608725-G-C
• rs17819128

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.139 in 152,188 control chromosomes in the GnomAD database, including 1,725 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 0.14 (1725 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.54

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 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: 0.139 AC: 21187 AN: 152070 Hom.: 1727 Cov.: 31

Gnomad AFR AF: 0.0713

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.139 AC: 21168 AN: 152188 Hom.: 1725 Cov.: 31 AF XY: 0.134 AC XY: 10003 AN XY: 74408

Gnomad4 AFR AF: 0.0712

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.157

Alfa AF: 0.147 Hom.: 224

Bravo AF: 0.136

Asia WGS AF: 0.126 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	16
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: rs17819128; hg19: chr12-12761659;