17-30325028-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_206832.3(TMIGD1):c.428G>A(p.Cys143Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,818 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. C143F) has been classified as Uncertain significance.
Frequency
Consequence
NM_206832.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMIGD1 | NM_206832.3 | c.428G>A | p.Cys143Tyr | missense_variant | Exon 4 of 7 | ENST00000328886.5 | NP_996663.1 | |
TMIGD1 | NM_001319942.2 | c.428G>A | p.Cys143Tyr | missense_variant | Exon 4 of 6 | NP_001306871.1 | ||
TMIGD1 | XM_011524787.2 | c.428G>A | p.Cys143Tyr | missense_variant | Exon 4 of 7 | XP_011523089.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMIGD1 | ENST00000328886.5 | c.428G>A | p.Cys143Tyr | missense_variant | Exon 4 of 7 | 1 | NM_206832.3 | ENSP00000332404.4 | ||
TMIGD1 | ENST00000538566.6 | c.428G>A | p.Cys143Tyr | missense_variant | Exon 4 of 6 | 2 | ENSP00000446118.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461818Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727210
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.