Variant chr8-100712798-C-CA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_002568.4(PABPC1):c.739-10_739-9insT variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 1,448,302 control chromosomes in the GnomAD database, including 12,982 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.22 ( 2602 hom., cov: 29)

Exomes 𝑓: 0.14 ( 10380 hom. )

Consequence

PABPC1
NM_002568.4 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.66

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 Benign. Variant got -10 ACMG points.

BP6

Variant 8-100712798-C-CA is Benign according to our data. Variant chr8-100712798-C-CA is described in ClinVar as [Benign]. Clinvar id is 770194.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
PABPC1	NM_002568.4 linkuse as main transcript	c.739-10_739-9insT	splice_polypyrimidine_tract_variant, intron_variant	ENST00000318607.10
PABPC1	XM_005250861.4 linkuse as main transcript	c.739-10_739-9insT	splice_polypyrimidine_tract_variant, intron_variant
PABPC1	XM_047421694.1 linkuse as main transcript	c.739-10_739-9insT	splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PABPC1	ENST00000318607.10 linkuse as main transcript	c.739-10_739-9insT		splice_polypyrimidine_tract_variant, intron_variant		1	NM_002568.4	P1	P11940-1

Frequencies

GnomAD3 genomes

AF:

0.218

AC:

26451

AN:

121468

Hom.:

2588

Cov.:

show subpopulations

Gnomad AFR

AF:

0.336

Gnomad AMI

AF:

0.182

Gnomad AMR

AF:

0.286

Gnomad ASJ

AF:

0.116

Gnomad EAS

AF:

0.330

Gnomad SAS

AF:

0.175

Gnomad FIN

AF:

0.174

Gnomad MID

AF:

0.112

Gnomad NFE

AF:

0.154

Gnomad OTH

AF:

0.190

GnomAD3 exomes

AF:

0.128

AC:

15099

AN:

118300

Hom.:

1091

AF XY:

0.121

AC XY:

7862

AN XY:

65134

show subpopulations

Gnomad AFR exome

AF:

0.223

Gnomad AMR exome

AF:

0.190

Gnomad ASJ exome

AF:

0.0691

Gnomad EAS exome

AF:

0.234

Gnomad SAS exome

AF:

0.110

Gnomad FIN exome

AF:

0.114

Gnomad NFE exome

AF:

0.102

Gnomad OTH exome

AF:

0.113

GnomAD4 exome

AF:

0.140

AC:

185264

AN:

1326784

Hom.:

10380

Cov.:

AF XY:

0.139

AC XY:

90931

AN XY:

655444

show subpopulations

Gnomad4 AFR exome

AF:

0.222

Gnomad4 AMR exome

AF:

0.221

Gnomad4 ASJ exome

AF:

0.109

Gnomad4 EAS exome

AF:

0.287

Gnomad4 SAS exome

AF:

0.142

Gnomad4 FIN exome

AF:

0.138

Gnomad4 NFE exome

AF:

0.130

Gnomad4 OTH exome

AF:

0.149

GnomAD4 genome

AF:

0.218

AC:

26490

AN:

121518

Hom.:

2602

Cov.:

AF XY:

0.224

AC XY:

13189

AN XY:

58808

show subpopulations

Gnomad4 AFR

AF:

0.336

Gnomad4 AMR

AF:

0.286

Gnomad4 ASJ

AF:

0.116

Gnomad4 EAS

AF:

0.330

Gnomad4 SAS

AF:

0.176

Gnomad4 FIN

AF:

0.174

Gnomad4 NFE

AF:

0.154

Gnomad4 OTH

AF:

0.192

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Aug 08, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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