rs13293285

chr9-112347020-A-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

PTBP3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
PTBP3	XM_047424271.1	c.-85-16546T>G		intron_variant
PTBP3	XM_047424272.1	c.-52+31680T>G		intron_variant
PTBP3	XM_047424273.1	c.-116-16546T>G		intron_variant
PTBP3	XM_047424274.1	c.-122-16546T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.396

Alfa AF: 0.357 Hom.: 3095

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13293285; hg19: chr9-115109300;