rs894157
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152259.4(TICRR):c.4567C>A(p.Arg1523Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1523H) has been classified as Uncertain significance.
Frequency
Consequence
NM_152259.4 missense
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 |
---|---|---|---|---|---|---|---|
TICRR | NM_152259.4 | c.4567C>A | p.Arg1523Ser | missense_variant | 20/22 | ENST00000268138.12 | |
TICRR | NM_001308025.1 | c.4564C>A | p.Arg1522Ser | missense_variant | 20/22 | ||
KIF7 | XM_047432481.1 | c.3847+3724G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TICRR | ENST00000268138.12 | c.4567C>A | p.Arg1523Ser | missense_variant | 20/22 | 5 | NM_152259.4 | A2 | |
TICRR | ENST00000560985.5 | c.4564C>A | p.Arg1522Ser | missense_variant | 20/22 | 1 | P4 | ||
KIF7 | ENST00000558928.1 | c.180+3724G>T | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome Cov.: 69
GnomAD4 genome ? Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at