12-57755616-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_138396.6(MARCHF9):c.88C>T(p.Pro30Ser) 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 1,344,132 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MARCHF9 | ENST00000266643.6 | c.88C>T | p.Pro30Ser | missense_variant | Exon 1 of 4 | 1 | NM_138396.6 | ENSP00000266643.5 | ||
CDK4 | ENST00000552862.1 | c.-20+316G>A | intron_variant | Intron 1 of 2 | 3 | ENSP00000446763.1 | ||||
MARCHF9 | ENST00000552279.1 | n.-112C>T | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 151612Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.000122 AC: 2AN: 16336Hom.: 0 AF XY: 0.000192 AC XY: 2AN XY: 10428
GnomAD4 exome AF: 0.000132 AC: 157AN: 1192414Hom.: 2 Cov.: 31 AF XY: 0.000118 AC XY: 69AN XY: 583392
GnomAD4 genome AF: 0.000152 AC: 23AN: 151718Hom.: 0 Cov.: 29 AF XY: 0.000202 AC XY: 15AN XY: 74124
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.88C>T (p.P30S) 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 88, causing the proline (P) at amino acid position 30 to be replaced by a serine (S). 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