15-56429102-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM4BP6_ModerateBS1BS2
The NM_018365.4(MNS1):c.1487G>T(p.Ter496Leuext*?) variant causes a stop lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000586 in 1,578,010 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_018365.4 stop_lost
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 |
---|---|---|---|---|---|---|---|---|---|---|
MNS1 | ENST00000260453.4 | c.1487G>T | p.Ter496Leuext*? | stop_lost | Exon 10 of 10 | 1 | NM_018365.4 | ENSP00000260453.3 | ||
TEX9 | ENST00000696102.1 | c.*658C>A | 3_prime_UTR_variant | Exon 12 of 12 | NM_001395496.1 | ENSP00000512397.1 |
Frequencies
GnomAD3 genomes AF: 0.00330 AC: 502AN: 152014Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000782 AC: 182AN: 232794Hom.: 0 AF XY: 0.000492 AC XY: 62AN XY: 126064
GnomAD4 exome AF: 0.000295 AC: 420AN: 1425878Hom.: 3 Cov.: 29 AF XY: 0.000246 AC XY: 175AN XY: 710066
GnomAD4 genome AF: 0.00331 AC: 504AN: 152132Hom.: 1 Cov.: 32 AF XY: 0.00321 AC XY: 239AN XY: 74380
ClinVar
Submissions by phenotype
not provided Benign:1
- -
MNS1-related disorder Benign:1
This variant is classified as 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