Variant chr8-100703359-T-TTTTAAACAGTTGGAACACCAGTGG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_002568.4(PABPC1):c.*2-1_*2insCCACTGGTGTTCCAACTGTTTAAA variant causes a splice region, 3 prime UTR change. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: 𝑓 0.00033 ( 0 hom., cov: 30)

Failed GnomAD Quality Control

Consequence

PABPC1
NM_002568.4 splice_region, 3_prime_UTR

Scores

Not classified

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: 6.03

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:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
PABPC1	NM_002568.4 linkuse as main transcript	c.2-1_2insCCACTGGTGTTCCAACTGTTTAAA	splice_region_variant, 3_prime_UTR_variant		ENST00000318607.10
PABPC1	XM_005250861.4 linkuse as main transcript	c.19-1_19insCCACTGGTGTTCCAACTGTTTAAA	splice_region_variant, 3_prime_UTR_variant
PABPC1	XM_047421694.1 linkuse as main transcript	c.938_939insCCACTGGTGTTCCAACTGTTTAAA	3_prime_UTR_variant	14/14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PABPC1	ENST00000318607.10 linkuse as main transcript	c.2-1_2insCCACTGGTGTTCCAACTGTTTAAA		splice_region_variant, 3_prime_UTR_variant		1	NM_002568.4	P1	P11940-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

146410

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.000405

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000405

Gnomad ASJ

AF:

0.000599

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000640

Gnomad FIN

AF:

0.000193

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000290

Gnomad OTH

AF:

0.00

GnomAD4 exome

Cov.:

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000328

AC:

AN:

146518

Hom.:

Cov.:

AF XY:

0.000390

AC XY:

AN XY:

71762

show subpopulations

Gnomad4 AFR

AF:

0.000404

Gnomad4 AMR

AF:

0.000404

Gnomad4 ASJ

AF:

0.000599

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000641

Gnomad4 FIN

AF:

0.000193

Gnomad4 NFE

AF:

0.000290

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.00662

Hom.:

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

LINK: link

Submissions by phenotype

CIC-rearranged sarcoma

Other:1

not provided, no classification provided

literature only

Children's Cancer Therapy Development Institute

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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