rs1587140774

Variant names:

• chr8-100703359-T-TTTTAAA
• rs1587140774
• NM_002568.4:c.*2-1_*2insTTTAAA

Your query was ambiguous. Multiple possible variants found:

• chr8-100703359-T-TTTTAAA
• chr8-100703359-T-TTTTAAACAGTTGGAACAC
• chr8-100703359-T-TTTTAAACAGTTGGAACACCAGTGG
• chr8-100703359-T-TTTTAAACAGTTGGAACACCAGTGGCG
• chr8-100703359-T-TTTTAAACAGTTGGAACACCGGTGG

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_Strong

The NM_002568.4(PABPC1):​c.*2-1_*2insTTTAAA variant causes a splice acceptor, intron change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000020 (0 hom., cov: 30)
  • Exomes 𝑓: 0.00029 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PABPC1 NM_002568.4 splice_acceptor, intron
• Clinical Significance: Not reported in ClinVar
• 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 4 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.23233908 fraction of the gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PABPC1	NM_002568.4	c.*2-1_*2insTTTAAA		splice_acceptor_variant, intron_variant	Intron 14 of 14	ENST00000318607.10	NP_002559.2
PABPC1	XM_047421694.1	c.*938_*939insTTTAAA		3_prime_UTR_variant	Exon 14 of 14		XP_047277650.1
PABPC1	XM_005250861.4	c.*19-1_*19insTTTAAA		splice_acceptor_variant, intron_variant	Intron 14 of 14		XP_005250918.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PABPC1	ENST00000318607.10	c.*2-1_*2insTTTAAA		splice_acceptor_variant, intron_variant	Intron 14 of 14	1	NM_002568.4	ENSP00000313007.5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 3 AN: 147902 Hom.: 0 Cov.: 30 FAILED QC

Gnomad AFR AF: 0.0000500

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000198

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

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000295 AC: 1 AN: 3394 Hom.: 0 Cov.: 0 AF XY: 0.000561 AC XY: 1 AN XY: 1782

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.000298

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000203 AC: 3 AN: 148008 Hom.: 0 Cov.: 30 AF XY: 0.0000276 AC XY: 2 AN XY: 72386

Gnomad4 AFR AF: 0.0000499

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000199

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Alfa AF: 0.00434 Hom.: 0

ClinVar

Not reported in ClinVar

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;