rs519384

Variant names:

• chr3-172450717-T-A
• rs519384

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 0.23 in 151,992 control chromosomes in the GnomAD database, including 4,670 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 (4670 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34871 AN: 151874 Hom.: 4661 Cov.: 32

Gnomad AFR AF: 0.0973

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.230 AC: 34905 AN: 151992 Hom.: 4670 Cov.: 32 AF XY: 0.232 AC XY: 17233 AN XY: 74288

African (AFR) AF: 0.0975 AC: 4040 AN: 41452

American (AMR) AF: 0.298 AC: 4547 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 552 AN: 3472

East Asian (EAS) AF: 0.376 AC: 1944 AN: 5172

South Asian (SAS) AF: 0.219 AC: 1055 AN: 4816

European-Finnish (FIN) AF: 0.293 AC: 3082 AN: 10530

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18948 AN: 67972

Other (OTH) AF: 0.219 AC: 462 AN: 2112

Alfa AF: 0.246 Hom.: 609

Bravo AF: 0.229

Asia WGS AF: 0.274 AC: 957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.48
PhyloP100		0.028

Splicing

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

Other links and lift over

dbSNP: rs519384; hg19: chr3-172168507;