chr8-100712798-CA-C

Variant names:

• chr8-100712798-CA-C
• rs34574721
• NM_002568.4:c.739-10delT

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.66

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 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
PABPC1	NM_002568.4	c.739-10delT		intron_variant	Intron 5 of 14	ENST00000318607.10	NP_002559.2
PABPC1	XM_005250861.4	c.739-10delT		intron_variant	Intron 5 of 14		XP_005250918.1
PABPC1	XM_047421694.1	c.739-10delT		intron_variant	Intron 5 of 13		XP_047277650.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PABPC1	ENST00000318607.10	c.739-10delT		intron_variant	Intron 5 of 14	1	NM_002568.4	ENSP00000313007.5

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

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

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

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

Other links and lift over

dbSNP: rs34574721; hg19: chr8-101725026;