15-56431494-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_018365.4(MNS1):c.1274G>A(p.Arg425His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00151 in 1,613,420 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_018365.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MNS1 | NM_018365.4 | c.1274G>A | p.Arg425His | missense_variant | 9/10 | ENST00000260453.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MNS1 | ENST00000260453.4 | c.1274G>A | p.Arg425His | missense_variant | 9/10 | 1 | NM_018365.4 | P1 | |
TEX9 | ENST00000352903.6 | c.*29+3021C>T | intron_variant | 1 | P1 | ||||
MNS1 | ENST00000566386.1 | n.75G>A | non_coding_transcript_exon_variant | 2/4 | 3 | ||||
TEX9 | ENST00000537232.5 | c.*1305+3021C>T | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00130 AC: 197AN: 152108Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00140 AC: 352AN: 250610Hom.: 1 AF XY: 0.00157 AC XY: 213AN XY: 135474
GnomAD4 exome AF: 0.00153 AC: 2235AN: 1461194Hom.: 5 Cov.: 30 AF XY: 0.00165 AC XY: 1197AN XY: 726904
GnomAD4 genome AF: 0.00134 AC: 204AN: 152226Hom.: 2 Cov.: 32 AF XY: 0.00130 AC XY: 97AN XY: 74416
ClinVar
Submissions by phenotype
MNS1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 20, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at