12-43844697-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032256.3(TMEM117):c.46A>G(p.Met16Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,461,848 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_032256.3 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 |
---|---|---|---|---|---|---|---|
TMEM117 | NM_032256.3 | c.46A>G | p.Met16Val | missense_variant | 2/8 | ENST00000266534.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM117 | ENST00000266534.8 | c.46A>G | p.Met16Val | missense_variant | 2/8 | 1 | NM_032256.3 | P1 | |
TMEM117 | ENST00000551577.5 | c.46A>G | p.Met16Val | missense_variant | 2/7 | 1 | |||
TMEM117 | ENST00000546868.5 | c.46A>G | p.Met16Val | missense_variant, NMD_transcript_variant | 2/7 | 1 | |||
TMEM117 | ENST00000546387.1 | n.304A>G | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251400Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135880
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461848Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727224
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 02, 2023 | The c.46A>G (p.M16V) alteration is located in exon 2 (coding exon 1) of the TMEM117 gene. This alteration results from a A to G substitution at nucleotide position 46, causing the methionine (M) at amino acid position 16 to be replaced by a valine (V). 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