chr10-28058545-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001318170.2(MPP7):c.1357C>T(p.Arg453Trp) variant causes a missense change. The variant allele was found at a frequency of 0.00000996 in 1,606,078 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R453Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001318170.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MPP7 | NM_001318170.2 | c.1357C>T | p.Arg453Trp | missense_variant | 15/17 | ENST00000683449.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MPP7 | ENST00000683449.1 | c.1357C>T | p.Arg453Trp | missense_variant | 15/17 | NM_001318170.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152172Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000405 AC: 1AN: 247042Hom.: 0 AF XY: 0.00000749 AC XY: 1AN XY: 133566
GnomAD4 exome AF: 0.00000894 AC: 13AN: 1453906Hom.: 0 Cov.: 29 AF XY: 0.00000691 AC XY: 5AN XY: 723244
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152172Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 11, 2021 | The c.1357C>T (p.R453W) alteration is located in exon 17 (coding exon 14) of the MPP7 gene. This alteration results from a C to T substitution at nucleotide position 1357, causing the arginine (R) at amino acid position 453 to be replaced by a tryptophan (W). 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