chr18-58671685-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_006785.4(MALT1):c.42G>C(p.Ser14=) 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. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. S14S) has been classified as Likely benign.
Frequency
Consequence
NM_006785.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MALT1 | NM_006785.4 | c.42G>C | p.Ser14= | synonymous_variant | 1/17 | ENST00000649217.2 | |
MALT1-AS1 | NR_164150.1 | n.189C>G | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MALT1 | ENST00000649217.2 | c.42G>C | p.Ser14= | synonymous_variant | 1/17 | NM_006785.4 | P3 | ||
MALT1-AS1 | ENST00000588144.2 | n.193C>G | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1097766Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 525084
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Combined immunodeficiency due to MALT1 deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 04, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.