rs572902669
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP7BS2
The NM_198994.3(TGM6):c.955C>A(p.Arg319=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,614,152 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 𝑓 0.000026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000021 ( 0 hom. )
Consequence
TGM6
NM_198994.3 synonymous
NM_198994.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.503
Genes affected
TGM6 (HGNC:16255): (transglutaminase 6) The protein encoded by this gene belongs to the transglutaminase superfamily. It catalyzes the cross-linking of proteins and the conjugation of polyamines to proteins. Mutations in this gene are associated with spinocerebellar ataxia type 35 (SCA35). Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.28).
BP7
?
Synonymous conserved (PhyloP=0.503 with no splicing effect.
BS2
?
High AC in GnomAdExome at 9 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TGM6 | NM_198994.3 | c.955C>A | p.Arg319= | synonymous_variant | 7/13 | ENST00000202625.7 | |
TGM6 | NM_001254734.2 | c.955C>A | p.Arg319= | synonymous_variant | 7/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TGM6 | ENST00000202625.7 | c.955C>A | p.Arg319= | synonymous_variant | 7/13 | 1 | NM_198994.3 | P1 | |
TGM6 | ENST00000381423.1 | c.955C>A | p.Arg319= | synonymous_variant | 7/12 | 1 | |||
TGM6 | ENST00000477505.1 | n.586C>A | non_coding_transcript_exon_variant | 4/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152164Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251206Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135802
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GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461870Hom.: 0 Cov.: 32 AF XY: 0.0000234 AC XY: 17AN XY: 727234
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GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74456
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ClinVar
Not reported inComputational scores
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Benign
Cadd
Benign
Dann
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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