rs35405862
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000447944.7(PNPT1):āc.944A>Gā(p.Lys315Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000784 in 1,542,178 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.0045 ( 9 hom., cov: 33)
Exomes š: 0.00037 ( 6 hom. )
Consequence
PNPT1
ENST00000447944.7 missense
ENST00000447944.7 missense
Scores
2
4
11
Clinical Significance
Conservation
PhyloP100: 7.03
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.010453165).
BP6
Variant 2-55671351-T-C is Benign according to our data. Variant chr2-55671351-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 214999.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00453 (690/152342) while in subpopulation AFR AF= 0.0161 (669/41584). AF 95% confidence interval is 0.0151. There are 9 homozygotes in gnomad4. There are 306 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PNPT1 | NM_033109.5 | c.944A>G | p.Lys315Arg | missense_variant | 11/28 | ENST00000447944.7 | NP_149100.2 | |
PNPT1 | XM_005264629.3 | c.704A>G | p.Lys235Arg | missense_variant | 11/28 | XP_005264686.1 | ||
PNPT1 | XM_017005172.2 | c.704A>G | p.Lys235Arg | missense_variant | 10/27 | XP_016860661.1 | ||
PNPT1 | XM_047446161.1 | c.944A>G | p.Lys315Arg | missense_variant | 11/20 | XP_047302117.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PNPT1 | ENST00000447944.7 | c.944A>G | p.Lys315Arg | missense_variant | 11/28 | 1 | NM_033109.5 | ENSP00000400646 | P1 | |
PNPT1 | ENST00000415374.5 | c.944A>G | p.Lys315Arg | missense_variant, NMD_transcript_variant | 11/29 | 5 | ENSP00000393953 | |||
PNPT1 | ENST00000415489.1 | c.20A>G | p.Lys7Arg | missense_variant, NMD_transcript_variant | 1/8 | 3 | ENSP00000411057 | |||
PNPT1 | ENST00000260604.8 | c.*499A>G | 3_prime_UTR_variant, NMD_transcript_variant | 10/27 | 5 | ENSP00000260604 |
Frequencies
GnomAD3 genomes AF: 0.00451 AC: 686AN: 152224Hom.: 9 Cov.: 33
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GnomAD3 exomes AF: 0.00100 AC: 216AN: 215022Hom.: 1 AF XY: 0.000716 AC XY: 84AN XY: 117342
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GnomAD4 exome AF: 0.000373 AC: 519AN: 1389836Hom.: 6 Cov.: 26 AF XY: 0.000311 AC XY: 215AN XY: 691080
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GnomAD4 genome AF: 0.00453 AC: 690AN: 152342Hom.: 9 Cov.: 33 AF XY: 0.00411 AC XY: 306AN XY: 74492
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jul 22, 2016 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 21, 2014 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
PNPT1-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 13, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
P
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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