8-100712798-CAAAAAA-C

Variant names:

• chr8-100712798-CAAAAAA-C
• rs34574721
• NM_002568.4:c.739-15_739-10delTTTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_002568.4(PABPC1):​c.739-15_739-10delTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000075 in 1,333,466 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: not found (cov: 29)
  • Exomes 𝑓: 7.5e-7 (0 hom.)
• Consequence: PABPC1 NM_002568.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.22
• Publications: 0 publications found

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]

ENSG00000310385 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002568.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PABPC1	NM_002568.4	MANE Select	c.739-15_739-10delTTTTTT		intron	N/A	NP_002559.2
	PABPC1	NM_001438282.1		c.739-15_739-10delTTTTTT		intron	N/A	NP_001425211.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PABPC1	ENST00000318607.10	TSL:1 MANE Select	c.739-15_739-10delTTTTTT		intron	N/A	ENSP00000313007.5	P11940-1
	PABPC1	ENST00000610907.2	TSL:1	c.595-15_595-10delTTTTTT		intron	N/A	ENSP00000478108.2	A0A087WTT1
	PABPC1	ENST00000900770.1		c.832-15_832-10delTTTTTT		intron	N/A	ENSP00000570829.1

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome AF: 7.50e-7 AC: 1 AN: 1333466 Hom.: 0 AF XY: 0.00000152 AC XY: 1 AN XY: 658856

African (AFR) AF: 0.00 AC: 0 AN: 28330

American (AMR) AF: 0.00 AC: 0 AN: 25982

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21622

East Asian (EAS) AF: 0.00 AC: 0 AN: 36496

South Asian (SAS) AF: 0.00 AC: 0 AN: 69140

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 48236

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5120

European-Non Finnish (NFE) AF: 9.58e-7 AC: 1 AN: 1043950

Other (OTH) AF: 0.00 AC: 0 AN: 54590

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.2

Splicing

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

Other links and lift over

dbSNP: rs34574721; hg19: chr8-101725026;