3-128625535-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 4P and 6B. PP3_StrongBP6_ModerateBS2
The NM_002950.4(RPN1):āc.1394A>Gā(p.Lys465Arg) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000699 in 1,613,576 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_002950.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPN1 | NM_002950.4 | c.1394A>G | p.Lys465Arg | missense_variant, splice_region_variant | 8/10 | ENST00000296255.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPN1 | ENST00000296255.8 | c.1394A>G | p.Lys465Arg | missense_variant, splice_region_variant | 8/10 | 1 | NM_002950.4 | P1 | |
RPN1 | ENST00000497289.5 | c.878A>G | p.Lys293Arg | missense_variant, splice_region_variant | 8/10 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00375 AC: 570AN: 151946Hom.: 6 Cov.: 31
GnomAD3 exomes AF: 0.000958 AC: 240AN: 250454Hom.: 3 AF XY: 0.000672 AC XY: 91AN XY: 135380
GnomAD4 exome AF: 0.000379 AC: 554AN: 1461512Hom.: 4 Cov.: 31 AF XY: 0.000333 AC XY: 242AN XY: 727070
GnomAD4 genome ? AF: 0.00377 AC: 574AN: 152064Hom.: 6 Cov.: 31 AF XY: 0.00352 AC XY: 262AN XY: 74336
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 30, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at