5-32233780-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001040446.3(MTMR12):c.1667G>A(p.Arg556His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000134 in 1,614,072 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 Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R556C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001040446.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTMR12 | NM_001040446.3 | c.1667G>A | p.Arg556His | missense_variant | Exon 15 of 16 | ENST00000382142.8 | NP_001035536.1 | |
MTMR12 | NM_001294343.2 | c.1512+1182G>A | intron_variant | Intron 14 of 14 | NP_001281272.1 | |||
MTMR12 | NM_001294344.2 | c.1345-3433G>A | intron_variant | Intron 13 of 13 | NP_001281273.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MTMR12 | ENST00000382142.8 | c.1667G>A | p.Arg556His | missense_variant | Exon 15 of 16 | 1 | NM_001040446.3 | ENSP00000371577.3 | ||
MTMR12 | ENST00000280285.9 | c.1512+1182G>A | intron_variant | Intron 14 of 14 | 1 | ENSP00000280285.5 | ||||
MTMR12 | ENST00000264934.5 | c.1345-3433G>A | intron_variant | Intron 13 of 13 | 2 | ENSP00000264934.5 | ||||
MTMR12 | ENST00000510216.1 | n.114G>A | non_coding_transcript_exon_variant | Exon 1 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000211 AC: 53AN: 251474Hom.: 0 AF XY: 0.000243 AC XY: 33AN XY: 135908
GnomAD4 exome AF: 0.000129 AC: 188AN: 1461890Hom.: 0 Cov.: 31 AF XY: 0.000142 AC XY: 103AN XY: 727244
GnomAD4 genome AF: 0.000184 AC: 28AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74334
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at