3-149333364-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_138786.4(TM4SF18):c.19G>A(p.Gly7Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000157 in 1,612,468 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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. G7E) has been classified as Uncertain significance.
Frequency
Consequence
NM_138786.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TM4SF18 | NM_138786.4 | c.19G>A | p.Gly7Arg | missense_variant | Exon 2 of 6 | ENST00000296059.7 | NP_620141.1 | |
TM4SF18 | NM_001184723.2 | c.19G>A | p.Gly7Arg | missense_variant | Exon 1 of 5 | NP_001171652.1 | ||
TM4SF18-AS1 | NR_186251.1 | n.405-140C>T | intron_variant | Intron 1 of 1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152116Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000760 AC: 19AN: 249984Hom.: 0 AF XY: 0.0000740 AC XY: 10AN XY: 135142
GnomAD4 exome AF: 0.000161 AC: 235AN: 1460352Hom.: 0 Cov.: 32 AF XY: 0.000147 AC XY: 107AN XY: 726412
GnomAD4 genome AF: 0.000118 AC: 18AN: 152116Hom.: 0 Cov.: 31 AF XY: 0.0000673 AC XY: 5AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.19G>A (p.G7R) alteration is located in exon 2 (coding exon 1) of the TM4SF18 gene. This alteration results from a G to A substitution at nucleotide position 19, causing the glycine (G) at amino acid position 7 to be replaced by an arginine (R). 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