Genetic Variant PCBP3:c.675+475C>T (chr21-45914500-C-T) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1

The NM_001348241.2(PCBP3):c.667C>T(p.Arg223*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 216,964 control chromosomes in the GnomAD database, including 24,459 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.47 ( 19136 hom., cov: 34)

Exomes 𝑓: 0.40 ( 5323 hom. )

Consequence

PCBP3
NM_001348241.2 stop_gained

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.0700

Variant links:

Genes affected

PCBP3 (HGNC:8651): (poly(rC) binding protein 3) This gene encodes a member of the KH-domain protein subfamily. Proteins of this subfamily, also referred to as alpha-CPs, bind to RNA with a specificity for C-rich pyrimidine regions. Alpha-CPs play important roles in post-transcriptional activities and have different cellular distributions. The protein encoded by this gene lacks the nuclear localization signals found in other subfamily members. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jan 2017]

PCBP3 links:

ENSG00000280604 (HGNC:):

ENSG00000280604 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6

Variant 21-45914500-C-T is Benign according to our data. Variant chr21-45914500-C-T is described in ClinVar as [Benign]. Clinvar id is 3060839.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCBP3	NM_001384156.1 link	c.675+475C>T		intron_variant	Intron 12 of 17	ENST00000681687.1	NP_001371085.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCBP3	ENST00000681687.1 link	c.675+475C>T		intron_variant	Intron 12 of 17		NM_001384156.1	ENSP00000505796.1		P57721-1

Frequencies

GnomAD3 genomes

AF:

0.473

AC:

71916

AN:

152050

Hom.:

19105

Cov.:

show subpopulations

Gnomad AFR

AF:

0.728

Gnomad AMI

AF:

0.363

Gnomad AMR

AF:

0.393

Gnomad ASJ

AF:

0.411

Gnomad EAS

AF:

0.325

Gnomad SAS

AF:

0.380

Gnomad FIN

AF:

0.327

Gnomad MID

AF:

0.557

Gnomad NFE

AF:

0.381

Gnomad OTH

AF:

0.443

GnomAD4 exome

AF:

0.396

AC:

25627

AN:

64796

Hom.:

5323

Cov.:

AF XY:

0.394

AC XY:

12693

AN XY:

32184

show subpopulations

Gnomad4 AFR exome

AF:

0.731

Gnomad4 AMR exome

AF:

0.346

Gnomad4 ASJ exome

AF:

0.411

Gnomad4 EAS exome

AF:

0.395

Gnomad4 SAS exome

AF:

0.362

Gnomad4 FIN exome

AF:

0.342

Gnomad4 NFE exome

AF:

0.382

Gnomad4 OTH exome

AF:

0.417

GnomAD4 genome

AF:

0.473

AC:

71985

AN:

152168

Hom.:

19136

Cov.:

AF XY:

0.467

AC XY:

34713

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.728

Gnomad4 AMR

AF:

0.393

Gnomad4 ASJ

AF:

0.411

Gnomad4 EAS

AF:

0.325

Gnomad4 SAS

AF:

0.379

Gnomad4 FIN

AF:

0.327

Gnomad4 NFE

AF:

0.381

Gnomad4 OTH

AF:

0.441

Alfa

AF:

0.422

Hom.:

1909

Bravo

AF:

0.491

Asia WGS

AF:

0.377

AC:

1315

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

PCBP3-related disorder

Benign:1

Oct 30, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.4

DANN

Benign

0.67

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over