chr2-227366083-A-G
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_024795.4(TM4SF20):c.401+10T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000325 in 1,609,960 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00028 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00033 ( 0 hom. )
Consequence
TM4SF20
NM_024795.4 intron
NM_024795.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0380
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 Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 2-227366083-A-G is Benign according to our data. Variant chr2-227366083-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1541296.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 43 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TM4SF20 | NM_024795.4 | c.401+10T>C | intron_variant | ENST00000304568.4 | |||
TM4SF20 | XM_011511876.3 | c.200+10T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TM4SF20 | ENST00000304568.4 | c.401+10T>C | intron_variant | 1 | NM_024795.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000283 AC: 43AN: 152176Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000194 AC: 48AN: 247288Hom.: 0 AF XY: 0.000232 AC XY: 31AN XY: 133696
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GnomAD4 exome AF: 0.000330 AC: 481AN: 1457666Hom.: 0 Cov.: 30 AF XY: 0.000331 AC XY: 240AN XY: 725036
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GnomAD4 genome AF: 0.000282 AC: 43AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74464
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 29, 2023 | - - |
Computational scores
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Benign
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Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at