chr9-13107002-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001378778.1(MPDZ):c.6176G>A(p.Arg2059Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00086 in 1,613,532 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R2059W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001378778.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MPDZ | NM_001378778.1 | c.6176G>A | p.Arg2059Gln | missense_variant | 47/47 | ENST00000319217.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MPDZ | ENST00000319217.12 | c.6176G>A | p.Arg2059Gln | missense_variant | 47/47 | 5 | NM_001378778.1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00471 AC: 717AN: 152116Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00123 AC: 307AN: 249260Hom.: 1 AF XY: 0.000895 AC XY: 121AN XY: 135222
GnomAD4 exome AF: 0.000460 AC: 672AN: 1461298Hom.: 3 Cov.: 30 AF XY: 0.000391 AC XY: 284AN XY: 726970
GnomAD4 genome ? AF: 0.00470 AC: 715AN: 152234Hom.: 5 Cov.: 32 AF XY: 0.00457 AC XY: 340AN XY: 74430
ClinVar
Submissions by phenotype
MPDZ-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 06, 2019 | 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). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 06, 2024 | - - |
Hydrocephalus, nonsyndromic, autosomal recessive 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 22, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at