12-57755724-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_138396.6(MARCHF9):c.196C>T(p.Arg66Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000328 in 1,219,822 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_138396.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MARCHF9 | ENST00000266643.6 | c.196C>T | p.Arg66Trp | missense_variant | Exon 1 of 4 | 1 | NM_138396.6 | ENSP00000266643.5 | ||
CDK4 | ENST00000552862.1 | c.-20+208G>A | intron_variant | Intron 1 of 2 | 3 | ENSP00000446763.1 | ||||
MARCHF9 | ENST00000552279.1 | n.-4C>T | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000133 AC: 2AN: 150068Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000187 AC: 2AN: 1069754Hom.: 0 Cov.: 33 AF XY: 0.00000393 AC XY: 2AN XY: 508734
GnomAD4 genome AF: 0.0000133 AC: 2AN: 150068Hom.: 0 Cov.: 31 AF XY: 0.0000273 AC XY: 2AN XY: 73212
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.196C>T (p.R66W) alteration is located in exon 1 (coding exon 1) of the MARCH9 gene. This alteration results from a C to T substitution at nucleotide position 196, causing the arginine (R) at amino acid position 66 to be replaced by a tryptophan (W). 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