15-56431424-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_018365.4(MNS1):c.1344G>T(p.Arg448Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,613,374 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018365.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MNS1 | ENST00000260453.4 | c.1344G>T | p.Arg448Ser | missense_variant | Exon 9 of 10 | 1 | NM_018365.4 | ENSP00000260453.3 | ||
TEX9 | ENST00000352903.6 | c.*29+2951C>A | intron_variant | Intron 12 of 12 | 1 | ENSP00000342169.2 | ||||
MNS1 | ENST00000566386.1 | n.145G>T | non_coding_transcript_exon_variant | Exon 2 of 4 | 3 | |||||
TEX9 | ENST00000537232.5 | n.*1305+2951C>A | intron_variant | Intron 12 of 12 | 2 | ENSP00000438745.2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 251026Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135688
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461262Hom.: 0 Cov.: 30 AF XY: 0.0000206 AC XY: 15AN XY: 726912
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1344G>T (p.R448S) alteration is located in exon 9 (coding exon 9) of the MNS1 gene. This alteration results from a G to T substitution at nucleotide position 1344, causing the arginine (R) at amino acid position 448 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