rs3830028
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_013364.6(PNMA3):c.*1122T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.93 ( 34065 hom., 30987 hem., cov: 23)
Exomes 𝑓: 0.98 ( 3747 hom. 3493 hem. )
Failed GnomAD Quality Control
Consequence
PNMA3
NM_013364.6 3_prime_UTR
NM_013364.6 3_prime_UTR
Scores
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -4.00
Genes affected
PNMA3 (HGNC:18742): (PNMA family member 3) The protein encoded by this gene belongs to the paraneoplastic antigen MA (PNMA) family, which shares homology with retroviral Gag proteins. The PNMA antigens are highly expressed in the brain and also in a range of tumors associated with serious neurological phenotypes. PMID:16407312 reports the presence of a functional -1 ribosomal frameshift signal (consisting of a heptanucleotide shift motif followed 3' by a pseudoknot structure) in this gene, however, the frame-shifted product has not been characterized. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]
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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=-0.93).
BA1
?
GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PNMA3 | NM_013364.6 | c.*1122T>C | 3_prime_UTR_variant | 2/2 | ENST00000593810.3 | ||
PNMA3 | NM_001282535.2 | c.*1025T>C | 3_prime_UTR_variant | 3/3 | |||
PNMA3 | XR_938508.4 | n.2277T>C | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PNMA3 | ENST00000593810.3 | c.*1122T>C | 3_prime_UTR_variant | 2/2 | NM_013364.6 | P1 | |||
PNMA3 | ENST00000619635.1 | c.*1025T>C | 3_prime_UTR_variant | 3/3 | 1 | ||||
PNMA3 | ENST00000424805.1 | c.*610T>C | 3_prime_UTR_variant, NMD_transcript_variant | 3/3 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.931 AC: 103475AN: 111090Hom.: 34070 Cov.: 23 AF XY: 0.930 AC XY: 30933AN XY: 33272
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GnomAD4 exome AF: 0.977 AC: 11164AN: 11431Hom.: 3747 Cov.: 0 AF XY: 0.978 AC XY: 3493AN XY: 3573
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GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.931 AC: 103516AN: 111144Hom.: 34065 Cov.: 23 AF XY: 0.930 AC XY: 30987AN XY: 33336
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Data not reliable, filtered out with message: InbreedingCoeff
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ClinVar
Not reported inComputational scores
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Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at