7-99908778-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_033091.3(TRIM4):c.524C>T(p.Thr175Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000281 in 1,614,072 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033091.3 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 |
---|---|---|---|---|---|---|---|
TRIM4 | NM_033091.3 | c.524C>T | p.Thr175Met | missense_variant | 3/6 | ENST00000349062.7 | |
TRIM4 | NM_033017.4 | c.602C>T | p.Thr201Met | missense_variant | 4/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM4 | ENST00000349062.7 | c.524C>T | p.Thr175Met | missense_variant | 3/6 | 1 | NM_033091.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000210 AC: 32AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000203 AC: 51AN: 251184Hom.: 0 AF XY: 0.000199 AC XY: 27AN XY: 135768
GnomAD4 exome AF: 0.000288 AC: 421AN: 1461836Hom.: 0 Cov.: 31 AF XY: 0.000293 AC XY: 213AN XY: 727222
GnomAD4 genome ? AF: 0.000210 AC: 32AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74438
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2022 | The c.602C>T (p.T201M) alteration is located in exon 4 (coding exon 4) of the TRIM4 gene. This alteration results from a C to T substitution at nucleotide position 602, causing the threonine (T) at amino acid position 201 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at