chr4-87493766-CCAT-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004684.6(SPARCL1):c.1031_1033del(p.Asp344del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Consequence
SPARCL1
NM_004684.6 inframe_deletion
NM_004684.6 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.257
Genes affected
SPARCL1 (HGNC:11220): (SPARC like 1) Predicted to enable calcium ion binding activity; collagen binding activity; and extracellular matrix binding activity. Predicted to be involved in anatomical structure development and regulation of synapse organization. Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPARCL1 | NM_004684.6 | c.1031_1033del | p.Asp344del | inframe_deletion | 4/11 | ENST00000282470.11 | |
SPARCL1 | NM_001128310.3 | c.1031_1033del | p.Asp344del | inframe_deletion | 5/12 | ||
SPARCL1 | NM_001291976.2 | c.656_658del | p.Asp219del | inframe_deletion | 5/12 | ||
SPARCL1 | NM_001291977.2 | c.656_658del | p.Asp219del | inframe_deletion | 3/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPARCL1 | ENST00000282470.11 | c.1031_1033del | p.Asp344del | inframe_deletion | 4/11 | 1 | NM_004684.6 | P2 | |
SPARCL1 | ENST00000418378.5 | c.1031_1033del | p.Asp344del | inframe_deletion | 5/12 | 5 | P2 | ||
SPARCL1 | ENST00000503414.5 | c.656_658del | p.Asp219del | inframe_deletion | 5/12 | 2 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SPARCL1-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 09, 2023 | The SPARCL1 c.1031_1033delATG variant is predicted to result in an in-frame deletion (p.Asp344del). To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Although we suspect that this variant may be pathogenic, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
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.