chr7-74338680-C-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_003388.5(CLIP2):c.354C>T(p.Gly118=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CLIP2
NM_003388.5 synonymous
NM_003388.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.00700
Genes affected
CLIP2 (HGNC:2586): (CAP-Gly domain containing linker protein 2) The protein encoded by this gene belongs to the family of cytoplasmic linker proteins, which have been proposed to mediate the interaction between specific membranous organelles and microtubules. This protein was found to associate with both microtubules and an organelle called the dendritic lamellar body. This gene is hemizygously deleted in Williams syndrome, a multisystem developmental disorder caused by the deletion of contiguous genes at 7q11.23. Alternative splicing of this gene generates 2 transcript variants. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
Variant 7-74338680-C-T is Benign according to our data. Variant chr7-74338680-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2673106.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.007 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| CLIP2 | NM_003388.5 | c.354C>T | p.Gly118= | synonymous_variant | 3/17 | ENST00000223398.11 | NP_003379.4 | |
| CLIP2 | NM_032421.3 | c.354C>T | p.Gly118= | synonymous_variant | 3/16 | NP_115797.2 | ||
| CLIP2 | XM_047420800.1 | c.354C>T | p.Gly118= | synonymous_variant | 3/13 | XP_047276756.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| CLIP2 | ENST00000223398.11 | c.354C>T | p.Gly118= | synonymous_variant | 3/17 | 5 | NM_003388.5 | ENSP00000223398 | P3 | |
| CLIP2 | ENST00000361545.9 | c.354C>T | p.Gly118= | synonymous_variant | 3/16 | 1 | ENSP00000355151 | A1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1429292Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 709096
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
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0
AN:
1429292
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Cov.:
33
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0
AN XY:
709096
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GnomAD4 genome
GnomAD4 genome
Cov.:
32
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 | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2023 | CLIP2: PM2:Supporting, BP4, BP7 - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Calibrated prediction
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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
Publications
No publications associated with this variant yet.