rs11687951
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022894.4(PAPOLG):c.694+1069G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,096 control chromosomes in the GnomAD database, including 5,033 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.25 ( 5033 hom., cov: 32)
Consequence
PAPOLG
NM_022894.4 intron
NM_022894.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.239
Genes affected
PAPOLG (HGNC:14982): (poly(A) polymerase gamma) This gene encodes a member of the poly(A) polymerase family which catalyzes template-independent extension of the 3' end of a DNA/RNA strand. This enzyme shares 60% identity to the well characterized poly(A) polymerase II (PAPII) at the amino acid level. These two enzymes have similar organization of structural and functional domains. This enzyme is exclusively localized in the nucleus and exhibits both nonspecific and CPSF (cleavage and polyadenylation specificity factor)/AAUAAA-dependent polyadenylation activity. This gene is located on chromosome 2 in contrast to the PAPII gene, which is located on chromosome 14. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAPOLG | NM_022894.4 | c.694+1069G>C | intron_variant | ENST00000238714.8 | |||
PAPOLG | XM_005264500.5 | c.694+1069G>C | intron_variant | ||||
PAPOLG | XM_005264501.3 | c.562+1069G>C | intron_variant | ||||
PAPOLG | XR_007080681.1 | n.905+1069G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAPOLG | ENST00000238714.8 | c.694+1069G>C | intron_variant | 1 | NM_022894.4 | P1 | |||
PAPOLG | ENST00000414060.5 | c.562+1069G>C | intron_variant, NMD_transcript_variant | 1 | |||||
PAPOLG | ENST00000453839.5 | c.*57+1069G>C | intron_variant, NMD_transcript_variant | 1 | |||||
PAPOLG | ENST00000496283.5 | n.662+1069G>C | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.248 AC: 37709AN: 151978Hom.: 5031 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.248 AC: 37724AN: 152096Hom.: 5033 Cov.: 32 AF XY: 0.251 AC XY: 18644AN XY: 74348
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at