chr12-94571512-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_020698.4(TMCC3):c.1357G>A(p.Val453Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 1,613,964 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020698.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMCC3 | NM_020698.4 | c.1357G>A | p.Val453Met | missense_variant | Exon 4 of 4 | ENST00000261226.9 | NP_065749.3 | |
TMCC3 | NM_001301036.2 | c.1264G>A | p.Val422Met | missense_variant | Exon 4 of 4 | NP_001287965.1 | ||
MIR7844 | NR_106998.1 | n.-160G>A | upstream_gene_variant | |||||
MIR7844 | unassigned_transcript_2046 | n.-185G>A | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMCC3 | ENST00000261226.9 | c.1357G>A | p.Val453Met | missense_variant | Exon 4 of 4 | 1 | NM_020698.4 | ENSP00000261226.4 | ||
TMCC3 | ENST00000551457.1 | c.1264G>A | p.Val422Met | missense_variant | Exon 4 of 4 | 1 | ENSP00000449888.1 | |||
MIR7844 | ENST00000616161.1 | n.-160G>A | upstream_gene_variant | 6 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152094Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251440Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135894
GnomAD4 exome AF: 0.0000280 AC: 41AN: 1461870Hom.: 0 Cov.: 31 AF XY: 0.0000261 AC XY: 19AN XY: 727238
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152094Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74284
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1357G>A (p.V453M) alteration is located in exon 4 (coding exon 4) of the TMCC3 gene. This alteration results from a G to A substitution at nucleotide position 1357, causing the valine (V) at amino acid position 453 to be replaced by a methionine (M). 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