8-38991538-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_078473.3(TM2D2):c.439G>A(p.Gly147Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,610,998 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_078473.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TM2D2 | NM_078473.3 | c.439G>A | p.Gly147Arg | missense_variant | 4/4 | ENST00000456397.7 | NP_510882.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TM2D2 | ENST00000456397.7 | c.439G>A | p.Gly147Arg | missense_variant | 4/4 | 1 | NM_078473.3 | ENSP00000416050 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152044Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251140Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135740
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1458954Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 726088
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152044Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74244
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 17, 2022 | The c.439G>A (p.G147R) alteration is located in exon 4 (coding exon 4) of the TM2D2 gene. This alteration results from a G to A substitution at nucleotide position 439, causing the glycine (G) at amino acid position 147 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