rs141383610
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001247997.2(CLIP1):c.297C>T(p.Asn99=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000234 in 1,613,850 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 0.0012 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00013 ( 0 hom. )
Consequence
CLIP1
NM_001247997.2 synonymous
NM_001247997.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.153
Genes affected
CLIP1 (HGNC:10461): (CAP-Gly domain containing linker protein 1) The protein encoded by this gene links endocytic vesicles to microtubules. This gene is highly expressed in Reed-Sternberg cells of Hodgkin disease. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
?
Variant 12-122377749-G-A is Benign according to our data. Variant chr12-122377749-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 434787.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.153 with no splicing effect.
BS2
?
High AC in GnomAd4 at 181 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLIP1 | NM_001247997.2 | c.297C>T | p.Asn99= | synonymous_variant | 3/26 | ENST00000620786.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLIP1 | ENST00000620786.5 | c.297C>T | p.Asn99= | synonymous_variant | 3/26 | 5 | NM_001247997.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00120 AC: 182AN: 151848Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000354 AC: 89AN: 251424Hom.: 0 AF XY: 0.000316 AC XY: 43AN XY: 135880
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GnomAD4 exome AF: 0.000134 AC: 196AN: 1461884Hom.: 0 Cov.: 31 AF XY: 0.000135 AC XY: 98AN XY: 727244
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GnomAD4 genome ? AF: 0.00119 AC: 181AN: 151966Hom.: 0 Cov.: 31 AF XY: 0.00125 AC XY: 93AN XY: 74296
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 02, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 13, 2018 | - - |
CLIP1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 28, 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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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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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