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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTBP3	XM_047424271.1	c.-85-16546T>G		intron_variant	Intron 1 of 14		XP_047280227.1
PTBP3	XM_047424272.1	c.-52+31680T>G		intron_variant	Intron 1 of 13		XP_047280228.1
PTBP3	XM_047424273.1	c.-116-16546T>G		intron_variant	Intron 1 of 13		XP_047280229.1
PTBP3	XM_047424274.1	c.-122-16546T>G		intron_variant	Intron 1 of 13		XP_047280230.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;