rs13293285

Variant names:

• chr9-112347020-A-C
• rs13293285
• XM_047424271.1:c.-85-16546T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047424271.1(PTBP3):​c.-85-16546T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,020 control chromosomes in the GnomAD database, including 10,583 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 0.37 (10583 hom., cov: 33)
• Consequence: PTBP3 XM_047424271.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• Publications: 2 publications found

Genes affected

PTBP3 (HGNC:10253): (polypyrimidine tract binding protein 3) The protein encoded by this gene binds RNA and is a regulator of cell differentiation. The encoded protein preferentially binds to poly(G) and poly(U) sequences in vitro. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.421 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: 0.369 AC: 56045 AN: 151902 Hom.: 10567 Cov.: 33

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.369 AC: 56109 AN: 152020 Hom.: 10583 Cov.: 33 AF XY: 0.375 AC XY: 27851 AN XY: 74294

African (AFR) AF: 0.390 AC: 16152 AN: 41442

American (AMR) AF: 0.400 AC: 6116 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1642 AN: 3468

East Asian (EAS) AF: 0.404 AC: 2091 AN: 5174

South Asian (SAS) AF: 0.436 AC: 2103 AN: 4820

European-Finnish (FIN) AF: 0.441 AC: 4643 AN: 10526

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22153 AN: 67988

Other (OTH) AF: 0.396 AC: 838 AN: 2114

Alfa AF: 0.356 Hom.: 3850

Bravo AF: 0.370

Asia WGS AF: 0.378 AC: 1317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.59
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs13293285; hg19: chr9-115109300;