Variant chr8-100709642-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6BP7

The NM_002568.4(PABPC1):c.1062C>T(p.Asn354=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0061 ( 0 hom., cov: 33)

Exomes 𝑓: 0.016 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

PABPC1
NM_002568.4 synonymous

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.641

Variant links:

Genes affected

PABPC1 (HGNC:8554): (poly(A) binding protein cytoplasmic 1) This gene encodes a poly(A) binding protein. The protein shuttles between the nucleus and cytoplasm and binds to the 3' poly(A) tail of eukaryotic messenger RNAs via RNA-recognition motifs. The binding of this protein to poly(A) promotes ribosome recruitment and translation initiation; it is also required for poly(A) shortening which is the first step in mRNA decay. The gene is part of a small gene family including three protein-coding genes and several pseudogenes.[provided by RefSeq, Aug 2010]

PABPC1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 8-100709642-G-A is Benign according to our data. Variant chr8-100709642-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3356872.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=0.641 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
PABPC1	NM_002568.4 linkuse as main transcript	c.1062C>T	p.Asn354=	synonymous_variant	8/15	ENST00000318607.10
PABPC1	XM_005250861.4 linkuse as main transcript	c.1062C>T	p.Asn354=	synonymous_variant	8/15
PABPC1	XM_047421694.1 linkuse as main transcript	c.1062C>T	p.Asn354=	synonymous_variant	8/14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PABPC1	ENST00000318607.10 linkuse as main transcript	c.1062C>T	p.Asn354=	synonymous_variant	8/15	1	NM_002568.4	P1	P11940-1

Frequencies

GnomAD3 genomes

AF:

0.00608

AC:

791

AN:

130016

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00787

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00546

Gnomad ASJ

AF:

0.00420

Gnomad EAS

AF:

0.00688

Gnomad SAS

AF:

0.00701

Gnomad FIN

AF:

0.00670

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00503

Gnomad OTH

AF:

0.0116

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0158

AC:

16450

AN:

1041800

Hom.:

Cov.:

AF XY:

0.0182

AC XY:

9327

AN XY:

513634

show subpopulations

Gnomad4 AFR exome

AF:

0.0348

Gnomad4 AMR exome

AF:

0.0687

Gnomad4 ASJ exome

AF:

0.0269

Gnomad4 EAS exome

AF:

0.0196

Gnomad4 SAS exome

AF:

0.0573

Gnomad4 FIN exome

AF:

0.0332

Gnomad4 NFE exome

AF:

0.00947

Gnomad4 OTH exome

AF:

0.0147

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00608

AC:

791

AN:

130114

Hom.:

Cov.:

AF XY:

0.00660

AC XY:

412

AN XY:

62386

show subpopulations

Gnomad4 AFR

AF:

0.00784

Gnomad4 AMR

AF:

0.00546

Gnomad4 ASJ

AF:

0.00420

Gnomad4 EAS

AF:

0.00689

Gnomad4 SAS

AF:

0.00702

Gnomad4 FIN

AF:

0.00670

Gnomad4 NFE

AF:

0.00503

Gnomad4 OTH

AF:

0.0114

Alfa

AF:

0.132

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

PABPC1-related condition

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Sep 16, 2024

This variant is classified as likely 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

-0.50

CADD

Benign

8.5

DANN

Benign

0.84

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