rs34574721

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_002568.4(PABPC1):​c.739-10delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,332,238 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 29)
Exomes 𝑓: 0.00011 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

PABPC1
NM_002568.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High AC in GnomAdExome4 at 142 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PABPC1NM_002568.4 linkc.739-10delT intron_variant Intron 5 of 14 ENST00000318607.10 NP_002559.2 P11940-1A0A024R9C1
PABPC1XM_005250861.4 linkc.739-10delT intron_variant Intron 5 of 14 XP_005250918.1 P11940-1A0A024R9C1
PABPC1XM_047421694.1 linkc.739-10delT intron_variant Intron 5 of 13 XP_047277650.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PABPC1ENST00000318607.10 linkc.739-10delT intron_variant Intron 5 of 14 1 NM_002568.4 ENSP00000313007.5 P11940-1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
121690
Hom.:
0
Cov.:
29
FAILED QC
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000448
AC:
53
AN:
118300
Hom.:
0
AF XY:
0.000384
AC XY:
25
AN XY:
65134
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00106
Gnomad ASJ exome
AF:
0.000768
Gnomad EAS exome
AF:
0.000364
Gnomad SAS exome
AF:
0.000417
Gnomad FIN exome
AF:
0.000399
Gnomad NFE exome
AF:
0.000392
Gnomad OTH exome
AF:
0.000781
GnomAD4 exome
AF:
0.000107
AC:
142
AN:
1332238
Hom.:
0
Cov.:
31
AF XY:
0.0000987
AC XY:
65
AN XY:
658234
show subpopulations
Gnomad4 AFR exome
AF:
0.0000353
Gnomad4 AMR exome
AF:
0.000655
Gnomad4 ASJ exome
AF:
0.0000926
Gnomad4 EAS exome
AF:
0.0000823
Gnomad4 SAS exome
AF:
0.000246
Gnomad4 FIN exome
AF:
0.000207
Gnomad4 NFE exome
AF:
0.0000825
Gnomad4 OTH exome
AF:
0.0000917
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
121690
Hom.:
0
Cov.:
29
AF XY:
0.00
AC XY:
0
AN XY:
58852
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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.

Other links and lift over

dbSNP: rs34574721; hg19: chr8-101725026; API