9-13123296-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001378778.1(MPDZ):āc.4810A>Gā(p.Thr1604Ala) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0028 in 1,601,152 control chromosomes in the GnomAD database, including 111 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
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 | UniProt |
---|---|---|---|---|---|---|---|
MPDZ | NM_001378778.1 | c.4810A>G | p.Thr1604Ala | missense_variant, splice_region_variant | 36/47 | ENST00000319217.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MPDZ | ENST00000319217.12 | c.4810A>G | p.Thr1604Ala | missense_variant, splice_region_variant | 36/47 | 5 | NM_001378778.1 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0154 AC: 2337AN: 152094Hom.: 55 Cov.: 32
GnomAD3 exomes AF: 0.00391 AC: 885AN: 226152Hom.: 20 AF XY: 0.00291 AC XY: 355AN XY: 122090
GnomAD4 exome AF: 0.00148 AC: 2139AN: 1448940Hom.: 56 Cov.: 30 AF XY: 0.00121 AC XY: 873AN XY: 719540
GnomAD4 genome AF: 0.0154 AC: 2338AN: 152212Hom.: 55 Cov.: 32 AF XY: 0.0143 AC XY: 1067AN XY: 74428
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 08, 2013 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at