chr9-13223593-G-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001378778.1(MPDZ):āc.511C>Gā(p.Gln171Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00256 in 1,612,108 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. Q171Q) has been classified as Likely benign.
Frequency
Consequence
NM_001378778.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MPDZ | NM_001378778.1 | c.511C>G | p.Gln171Glu | missense_variant | 5/47 | ENST00000319217.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MPDZ | ENST00000319217.12 | c.511C>G | p.Gln171Glu | missense_variant | 5/47 | 5 | NM_001378778.1 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00172 AC: 262AN: 152042Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00165 AC: 409AN: 248362Hom.: 2 AF XY: 0.00155 AC XY: 209AN XY: 134736
GnomAD4 exome AF: 0.00265 AC: 3862AN: 1459946Hom.: 6 Cov.: 30 AF XY: 0.00255 AC XY: 1851AN XY: 726268
GnomAD4 genome AF: 0.00172 AC: 262AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.00157 AC XY: 117AN XY: 74382
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | MPDZ: BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 20, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at