rs17819128

Variant names:

• chr12-12608725-G-C
• rs17819128

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0712 AC: 2957 AN: 41528

American (AMR) AF: 0.104 AC: 1596 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 669 AN: 3468

East Asian (EAS) AF: 0.132 AC: 684 AN: 5174

South Asian (SAS) AF: 0.182 AC: 878 AN: 4828

European-Finnish (FIN) AF: 0.102 AC: 1080 AN: 10600

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12790 AN: 67986

Other (OTH) AF: 0.157 AC: 331 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	16
DANN	Benign	0.86
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs17819128; hg19: chr12-12761659;