NM_004237.4:c.123T>C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_004237.4(TRIP13):āc.123T>Cā(p.Ser41Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,611,178 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 (ā ).
Frequency
Consequence
NM_004237.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRIP13 | NM_004237.4 | c.123T>C | p.Ser41Ser | synonymous_variant | Exon 2 of 13 | ENST00000166345.8 | NP_004228.1 | |
TRIP13 | NM_001166260.2 | c.123T>C | p.Ser41Ser | synonymous_variant | Exon 2 of 9 | NP_001159732.1 | ||
TRIP13 | XM_011514163.2 | c.123T>C | p.Ser41Ser | synonymous_variant | Exon 2 of 14 | XP_011512465.1 | ||
TRIP13 | XM_047417879.1 | c.-337T>C | 5_prime_UTR_variant | Exon 2 of 13 | XP_047273835.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRIP13 | ENST00000166345.8 | c.123T>C | p.Ser41Ser | synonymous_variant | Exon 2 of 13 | 1 | NM_004237.4 | ENSP00000166345.3 | ||
TRIP13 | ENST00000512024.5 | n.238T>C | non_coding_transcript_exon_variant | Exon 2 of 9 | 1 | |||||
TRIP13 | ENST00000513435.1 | c.108T>C | p.Ser36Ser | synonymous_variant | Exon 2 of 8 | 5 | ENSP00000427528.1 | |||
TRIP13 | ENST00000508456.1 | n.97T>C | non_coding_transcript_exon_variant | Exon 2 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000804 AC: 2AN: 248790Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134260
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1459030Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 725330
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152148Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74334
ClinVar
Submissions by phenotype
TRIP13-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at