8-100703359-T-TTTTAAACAGTTGGAACACCAGTGG

Position:

• chr8-100703359-T-TTTTAAACAGTTGGAACACCAGTGG

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
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 6.03

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PABPC1	NM_002568.4	c.*2-1_*2insCCACTGGTGTTCCAACTGTTTAAA		splice_region_variant, 3_prime_UTR_variant		ENST00000318607.10
PABPC1	XM_005250861.4	c.*19-1_*19insCCACTGGTGTTCCAACTGTTTAAA		splice_region_variant, 3_prime_UTR_variant
PABPC1	XM_047421694.1	c.*938_*939insCCACTGGTGTTCCAACTGTTTAAA		3_prime_UTR_variant	14/14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PABPC1	ENST00000318607.10	c.*2-1_*2insCCACTGGTGTTCCAACTGTTTAAA		splice_region_variant, 3_prime_UTR_variant		1	NM_002568.4	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 48 AN: 146410 Hom.: 0 Cov.: 30 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.: 0

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000328 AC: 48 AN: 146518 Hom.: 0 Cov.: 30 AF XY: 0.000390 AC XY: 28 AN XY: 71762

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.: 0

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

CIC-rearranged sarcoma Other:1

not provided, no classification provided

literature only

Children's Cancer Therapy Development Institute

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1587140774; hg19: chr8-101715587;