chr4-80202599-C-T
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_001099403.2(PRDM8):c.1137C>T(p.Gly379=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PRDM8
NM_001099403.2 synonymous
NM_001099403.2 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.00300
Genes affected
PRDM8 (HGNC:13993): (PR/SET domain 8) This gene encodes a protein that belongs to a conserved family of histone methyltransferases that predominantly act as negative regulators of transcription. The encoded protein contains an N-terminal Su(var)3-9, Enhancer-of-zeste, and Trithorax (SET) domain and a double zinc-finger domain. Knockout of this gene in mouse results in mistargeting by neurons of the dorsal telencephalon, abnormal itch-like behavior, and impaired differentiation of rod bipolar cells. In humans, the protein has been shown to interact with the phosphatase laforin and the ubiquitin ligase malin, which regulate glycogen construction in the cytoplasm. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP7
Synonymous conserved (PhyloP=-0.003 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRDM8 | NM_001099403.2 | c.1137C>T | p.Gly379= | synonymous_variant | 4/4 | ENST00000415738.3 | NP_001092873.1 | |
PRDM8 | NM_020226.4 | c.1137C>T | p.Gly379= | synonymous_variant | 10/10 | NP_064611.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRDM8 | ENST00000415738.3 | c.1137C>T | p.Gly379= | synonymous_variant | 4/4 | 1 | NM_001099403.2 | ENSP00000406998 | P1 | |
PRDM8 | ENST00000339711.8 | c.1137C>T | p.Gly379= | synonymous_variant | 10/10 | 1 | ENSP00000339764 | P1 | ||
PRDM8 | ENST00000515013.5 | c.1137C>T | p.Gly379= | synonymous_variant | 10/10 | 1 | ENSP00000425149 | |||
PRDM8 | ENST00000504452.5 | c.1137C>T | p.Gly379= | synonymous_variant | 8/8 | 5 | ENSP00000423985 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1380270Hom.: 0 Cov.: 37 AF XY: 0.00 AC XY: 0AN XY: 681086
GnomAD4 exome
Data not reliable, filtered out with message: AC0
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0
AN:
1380270
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Cov.:
37
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0
AN XY:
681086
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at