3-33543456-T-C
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_001365631.1(CLASP2):āc.3381A>Gā(p.Thr1127Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000254 in 1,604,240 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: š 0.00017 ( 0 hom., cov: 32)
Exomes š: 0.00026 ( 4 hom. )
Consequence
CLASP2
NM_001365631.1 synonymous
NM_001365631.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.362
Genes affected
CLASP2 (HGNC:17078): (cytoplasmic linker associated protein 2) Enables cytoskeletal protein binding activity; dystroglycan binding activity; and protein tyrosine kinase binding activity. Involved in several processes, including microtubule cytoskeleton organization; positive regulation of extracellular matrix organization; and regulation of supramolecular fiber organization. Located in several cellular components, including basal cortex; cortical microtubule plus-end; and ruffle membrane. Colocalizes with focal adhesion; kinetochore; and microtubule cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.49).
BP6
Variant 3-33543456-T-C is Benign according to our data. Variant chr3-33543456-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3040123.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=0.362 with no splicing effect.
BS2
High AC in GnomAd4 at 26 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLASP2 | NM_001365631.1 | c.3381A>G | p.Thr1127Thr | synonymous_variant | 32/39 | ENST00000682230.1 | NP_001352560.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLASP2 | ENST00000682230.1 | c.3381A>G | p.Thr1127Thr | synonymous_variant | 32/39 | NM_001365631.1 | ENSP00000507498.1 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152172Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000465 AC: 116AN: 249230Hom.: 1 AF XY: 0.000695 AC XY: 94AN XY: 135202
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GnomAD4 exome AF: 0.000262 AC: 381AN: 1451950Hom.: 4 Cov.: 28 AF XY: 0.000412 AC XY: 298AN XY: 723128
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GnomAD4 genome AF: 0.000171 AC: 26AN: 152290Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74468
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
CLASP2-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 19, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Benign
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Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at