chr19-4294669-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001169126.2(TMIGD2):c.460G>A(p.Val154Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000691 in 1,590,962 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V154L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001169126.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMIGD2 | NM_001169126.2 | c.460G>A | p.Val154Met | missense_variant | 4/5 | ENST00000595645.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMIGD2 | ENST00000595645.6 | c.460G>A | p.Val154Met | missense_variant | 4/5 | 1 | NM_001169126.2 | A2 | |
TMIGD2 | ENST00000301272.6 | c.460G>A | p.Val154Met | missense_variant | 4/5 | 1 | P2 | ||
TMIGD2 | ENST00000600114.5 | c.100G>A | p.Val34Met | missense_variant | 3/4 | 1 | |||
TMIGD2 | ENST00000600349.1 | c.47-1784G>A | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151882Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000131 AC: 3AN: 228622Hom.: 0 AF XY: 0.0000162 AC XY: 2AN XY: 123196
GnomAD4 exome AF: 0.00000556 AC: 8AN: 1439080Hom.: 0 Cov.: 34 AF XY: 0.00000560 AC XY: 4AN XY: 714312
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151882Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 74148
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at