rs61743613
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_018451.5(CENPJ):c.1908C>T(p.Arg636=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,613,274 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. R636R) has been classified as Likely benign.
Frequency
Consequence
NM_018451.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CENPJ | NM_018451.5 | c.1908C>T | p.Arg636= | synonymous_variant | 7/17 | ENST00000381884.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CENPJ | ENST00000381884.9 | c.1908C>T | p.Arg636= | synonymous_variant | 7/17 | 1 | NM_018451.5 | P1 | |
CENPJ | ENST00000616936.4 | c.1908C>T | p.Arg636= | synonymous_variant, NMD_transcript_variant | 7/16 | 1 | |||
CENPJ | ENST00000545981.6 | c.1908C>T | p.Arg636= | synonymous_variant, NMD_transcript_variant | 7/18 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250978Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135624
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461086Hom.: 0 Cov.: 34 AF XY: 0.00000413 AC XY: 3AN XY: 726674
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152188Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74358
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 23, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at