chr9-13219604-C-G
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001378778.1(MPDZ):āc.1041G>Cā(p.Leu347Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00406 in 1,612,262 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MPDZ | NM_001378778.1 | c.1041G>C | p.Leu347Phe | missense_variant | Exon 8 of 47 | ENST00000319217.12 | NP_001365707.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00297 AC: 451AN: 151858Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00285 AC: 708AN: 248226Hom.: 3 AF XY: 0.00296 AC XY: 399AN XY: 134716
GnomAD4 exome AF: 0.00417 AC: 6091AN: 1460286Hom.: 19 Cov.: 32 AF XY: 0.00407 AC XY: 2957AN XY: 726444
GnomAD4 genome AF: 0.00297 AC: 451AN: 151976Hom.: 2 Cov.: 32 AF XY: 0.00287 AC XY: 213AN XY: 74258
ClinVar
Submissions by phenotype
not provided Benign:5
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MPDZ: BP4, BS2 -
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Hydrocephalus, nonsyndromic, autosomal recessive 2 Uncertain:1
This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. -
not specified Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at