chr2-55636078-A-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_033109.5(PNPT1):c.*159T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0035 in 412,252 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0029 ( 6 hom., cov: 33)
Exomes 𝑓: 0.0038 ( 5 hom. )
Consequence
PNPT1
NM_033109.5 3_prime_UTR
NM_033109.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.138
Genes affected
PNPT1 (HGNC:23166): (polyribonucleotide nucleotidyltransferase 1) The protein encoded by this gene belongs to the evolutionary conserved polynucleotide phosphorylase family comprised of phosphate dependent 3'-to-5' exoribonucleases implicated in RNA processing and degradation. This enzyme is predominantly localized in the mitochondrial intermembrane space and is involved in import of RNA to mitochondria. Mutations in this gene have been associated with combined oxidative phosphorylation deficiency-13 and autosomal recessive nonsyndromic deafness-70. Related pseudogenes are found on chromosomes 3 and 7. [provided by RefSeq, Dec 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
?
Variant 2-55636078-A-T is Benign according to our data. Variant chr2-55636078-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 1201859.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 6 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PNPT1 | NM_033109.5 | c.*159T>A | 3_prime_UTR_variant | 28/28 | ENST00000447944.7 | ||
PNPT1 | XM_005264629.3 | c.*159T>A | 3_prime_UTR_variant | 28/28 | |||
PNPT1 | XM_017005172.2 | c.*159T>A | 3_prime_UTR_variant | 27/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PNPT1 | ENST00000447944.7 | c.*159T>A | 3_prime_UTR_variant | 28/28 | 1 | NM_033109.5 | P1 | ||
PNPT1 | ENST00000260604.8 | c.*2053T>A | 3_prime_UTR_variant, NMD_transcript_variant | 27/27 | 5 | ||||
PNPT1 | ENST00000415374.5 | c.*159T>A | 3_prime_UTR_variant, NMD_transcript_variant | 28/29 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00295 AC: 449AN: 152168Hom.: 6 Cov.: 33
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GnomAD4 exome AF: 0.00382 AC: 992AN: 259966Hom.: 5 Cov.: 4 AF XY: 0.00380 AC XY: 503AN XY: 132472
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GnomAD4 genome ? AF: 0.00295 AC: 449AN: 152286Hom.: 6 Cov.: 33 AF XY: 0.00325 AC XY: 242AN XY: 74472
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 08, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at