chr2-227363807-CCTCCAGAAT-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM4
The NM_024795.4(TM4SF20):c.598_606del(p.Ile200_Glu202del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.0000118 in 1,614,140 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000012 ( 0 hom. )
Consequence
TM4SF20
NM_024795.4 inframe_deletion
NM_024795.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.69
Genes affected
TM4SF20 (HGNC:26230): (transmembrane 4 L six family member 20) The protein encoded by this gene is a member of the four-transmembrane L6 superfamily. Members of this family function in various cellular processes including cell proliferation, motility, and adhesion via their interactions with integrins. In human brain tissue, this gene is expressed at high levels in the parietal lobe, occipital lobe, hippocampus, pons, white matter, corpus callosum, and cerebellum. Knockout of the homologous gene in mouse results in a neurobehavioral phenotype with suggested enhanced motor coordination. A deletion mutation in the human gene is associated with specific language impairment-5. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM4
?
Nonframeshift variant in NON repetitive region in NM_024795.4.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TM4SF20 | NM_024795.4 | c.598_606del | p.Ile200_Glu202del | inframe_deletion | 4/4 | ENST00000304568.4 | |
TM4SF20 | XM_011511876.3 | c.397_405del | p.Ile133_Glu135del | inframe_deletion | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TM4SF20 | ENST00000304568.4 | c.598_606del | p.Ile200_Glu202del | inframe_deletion | 4/4 | 1 | NM_024795.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152136Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251484Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135916
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GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461886Hom.: 0 AF XY: 0.0000124 AC XY: 9AN XY: 727242
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GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152254Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74438
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | May 16, 2021 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals with TM4SF20-related conditions. This variant is present in population databases (rs749661328, ExAC 0.006%). This variant, c.598_606del, results in the deletion of 3 amino acid(s) of the TM4SF20 protein (p.Ile200_Glu202del), but otherwise preserves the integrity of the reading frame. - |
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at