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. R1523C) has been classified as Likely benign.
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TICRR | NM_152259.4 | c.4567C>A | p.Arg1523Ser | missense_variant | Exon 20 of 22 | ENST00000268138.12 | NP_689472.3 | |
TICRR | NM_001308025.1 | c.4564C>A | p.Arg1522Ser | missense_variant | Exon 20 of 22 | NP_001294954.1 | ||
KIF7 | XM_047432481.1 | c.3847+3724G>T | intron_variant | Intron 19 of 19 | XP_047288437.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TICRR | ENST00000268138.12 | c.4567C>A | p.Arg1523Ser | missense_variant | Exon 20 of 22 | 5 | NM_152259.4 | ENSP00000268138.7 | ||
TICRR | ENST00000560985.5 | c.4564C>A | p.Arg1522Ser | missense_variant | Exon 20 of 22 | 1 | ENSP00000453306.1 | |||
KIF7 | ENST00000558928.1 | n.178+3724G>T | intron_variant | Intron 1 of 2 | 3 | ENSP00000504283.1 |
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