rs3808880

Variant names:

• chr9-112299168-G-A
• rs3808880
• NM_001163788.4:c.-51-1252C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001163788.4(PTBP3):​c.-51-1252C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,086 control chromosomes in the GnomAD database, including 6,679 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 0.27 (6679 hom., cov: 33)
• Consequence: PTBP3 NM_001163788.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 1 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTBP3	NM_001163788.4	c.-51-1252C>T		intron_variant	Intron 1 of 13	ENST00000374257.6	NP_001157260.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTBP3	ENST00000374257.6	c.-51-1252C>T		intron_variant	Intron 1 of 13	2	NM_001163788.4	ENSP00000363375.1

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40404 AN: 151968 Hom.: 6681 Cov.: 33

Gnomad AFR AF: 0.0692

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.266 AC: 40410 AN: 152086 Hom.: 6679 Cov.: 33 AF XY: 0.275 AC XY: 20450 AN XY: 74336

African (AFR) AF: 0.0690 AC: 2863 AN: 41508

American (AMR) AF: 0.350 AC: 5352 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1520 AN: 3468

East Asian (EAS) AF: 0.373 AC: 1931 AN: 5176

South Asian (SAS) AF: 0.406 AC: 1958 AN: 4818

European-Finnish (FIN) AF: 0.447 AC: 4720 AN: 10570

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21050 AN: 67952

Other (OTH) AF: 0.312 AC: 658 AN: 2112

Alfa AF: 0.285 Hom.: 941

Bravo AF: 0.254

Asia WGS AF: 0.326 AC: 1128 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	3.4
DANN	Benign	0.80
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3808880; hg19: chr9-115061448;