10-87505267-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The ENST00000371996.9(MINPP1):c.352G>A(p.Gly118Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,459,122 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000371996.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MINPP1 | NM_004897.5 | c.352G>A | p.Gly118Arg | missense_variant | 1/5 | ENST00000371996.9 | NP_004888.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MINPP1 | ENST00000371996.9 | c.352G>A | p.Gly118Arg | missense_variant | 1/5 | 1 | NM_004897.5 | ENSP00000361064 | P1 | |
MINPP1 | ENST00000371994.8 | c.352G>A | p.Gly118Arg | missense_variant | 1/3 | 1 | ENSP00000361062 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000809 AC: 2AN: 247172Hom.: 0 AF XY: 0.00000745 AC XY: 1AN XY: 134236
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1459122Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 725394
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 29, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at