rs4144422
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006413.5(RPP30):c.432+29A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 1,388,106 control chromosomes in the GnomAD database, including 33,026 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 0.26 ( 5907 hom., cov: 32)
Exomes 𝑓: 0.20 ( 27119 hom. )
Consequence
RPP30
NM_006413.5 intron
NM_006413.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.114
Genes affected
RPP30 (HGNC:17688): (ribonuclease P/MRP subunit p30) Enables ribonuclease P RNA binding activity. Contributes to ribonuclease P activity. Involved in tRNA 5'-leader removal. Part of multimeric ribonuclease P complex and ribonuclease MRP complex. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPP30 | NM_006413.5 | c.432+29A>G | intron_variant | ENST00000371703.8 | |||
RPP30 | NM_001104546.2 | c.432+29A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPP30 | ENST00000371703.8 | c.432+29A>G | intron_variant | 1 | NM_006413.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.260 AC: 39553AN: 152016Hom.: 5890 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
39553
AN:
152016
Hom.:
Cov.:
32
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:
GnomAD3 exomes AF: 0.213 AC: 45537AN: 213832Hom.: 5208 AF XY: 0.212 AC XY: 24764AN XY: 116650
GnomAD3 exomes
AF:
AC:
45537
AN:
213832
Hom.:
AF XY:
AC XY:
24764
AN XY:
116650
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.204 AC: 252522AN: 1235972Hom.: 27119 Cov.: 16 AF XY: 0.205 AC XY: 128297AN XY: 624374
GnomAD4 exome
AF:
AC:
252522
AN:
1235972
Hom.:
Cov.:
16
AF XY:
AC XY:
128297
AN XY:
624374
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: 0.260 AC: 39615AN: 152134Hom.: 5907 Cov.: 32 AF XY: 0.257 AC XY: 19101AN XY: 74386
GnomAD4 genome
?
AF:
AC:
39615
AN:
152134
Hom.:
Cov.:
32
AF XY:
AC XY:
19101
AN XY:
74386
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:
685
AN:
3468
ClinVar
Not reported inComputational 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