chr2-55636166-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_033109.5(PNPT1):c.*71T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00546 in 1,108,716 control chromosomes in the GnomAD database, including 240 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.024 ( 149 hom., cov: 33)
Exomes 𝑓: 0.0025 ( 91 hom. )
Consequence
PNPT1
NM_033109.5 3_prime_UTR
NM_033109.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.560
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 2-55636166-A-G is Benign according to our data. Variant chr2-55636166-A-G is described in ClinVar as [Benign]. Clinvar id is 1261362.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0801 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PNPT1 | NM_033109.5 | c.*71T>C | 3_prime_UTR_variant | 28/28 | ENST00000447944.7 | ||
PNPT1 | XM_005264629.3 | c.*71T>C | 3_prime_UTR_variant | 28/28 | |||
PNPT1 | XM_017005172.2 | c.*71T>C | 3_prime_UTR_variant | 27/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PNPT1 | ENST00000447944.7 | c.*71T>C | 3_prime_UTR_variant | 28/28 | 1 | NM_033109.5 | P1 | ||
PNPT1 | ENST00000260604.8 | c.*1965T>C | 3_prime_UTR_variant, NMD_transcript_variant | 27/27 | 5 | ||||
PNPT1 | ENST00000415374.5 | c.*71T>C | 3_prime_UTR_variant, NMD_transcript_variant | 28/29 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0239 AC: 3629AN: 152114Hom.: 149 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
3629
AN:
152114
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00253 AC: 2419AN: 956484Hom.: 91 Cov.: 12 AF XY: 0.00217 AC XY: 1046AN XY: 481068
GnomAD4 exome
AF:
AC:
2419
AN:
956484
Hom.:
Cov.:
12
AF XY:
AC XY:
1046
AN XY:
481068
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0239 AC: 3634AN: 152232Hom.: 149 Cov.: 33 AF XY: 0.0229 AC XY: 1708AN XY: 74466
GnomAD4 genome
?
AF:
AC:
3634
AN:
152232
Hom.:
Cov.:
33
AF XY:
AC XY:
1708
AN XY:
74466
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
18
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 27, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at