rs34605667
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001378778.1(MPDZ):c.5723G>A(p.Arg1908Lys) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0386 in 1,613,092 control chromosomes in the GnomAD database, including 1,421 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001378778.1 missense, splice_region
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MPDZ | NM_001378778.1 | c.5723G>A | p.Arg1908Lys | missense_variant, splice_region_variant | 43/47 | ENST00000319217.12 | NP_001365707.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MPDZ | ENST00000319217.12 | c.5723G>A | p.Arg1908Lys | missense_variant, splice_region_variant | 43/47 | 5 | NM_001378778.1 | ENSP00000320006.7 |
Frequencies
GnomAD3 genomes AF: 0.0307 AC: 4666AN: 152138Hom.: 111 Cov.: 33
GnomAD3 exomes AF: 0.0328 AC: 8174AN: 249038Hom.: 167 AF XY: 0.0335 AC XY: 4527AN XY: 135092
GnomAD4 exome AF: 0.0394 AC: 57521AN: 1460836Hom.: 1310 Cov.: 31 AF XY: 0.0388 AC XY: 28231AN XY: 726700
GnomAD4 genome AF: 0.0306 AC: 4665AN: 152256Hom.: 111 Cov.: 33 AF XY: 0.0316 AC XY: 2353AN XY: 74446
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 08, 2013 | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at