chr6-168441433-T-G
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001166412.2(SMOC2):āc.63T>Gā(p.Ala21=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 1,507,100 control chromosomes in the GnomAD database, including 36,751 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.29 ( 8327 hom., cov: 33)
Exomes š: 0.18 ( 28424 hom. )
Consequence
SMOC2
NM_001166412.2 synonymous
NM_001166412.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.212
Genes affected
SMOC2 (HGNC:20323): (SPARC related modular calcium binding 2) This gene encodes a member of the SPARC family (secreted protein acidic and rich in cysteine/osteonectin/BM-40), which are highly expressed during embryogenesis and wound healing. The gene product is a matricellular protein which promotes matrix assembly and can stimulate endothelial cell proliferation and migration, as well as angiogenic activity. Associated with pulmonary function, this secretory gene product contains a Kazal domain, two thymoglobulin type-1 domains, and two EF-hand calcium-binding domains. The encoded protein may serve as a target for controlling angiogenesis in tumor growth and myocardial ischemia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
Variant 6-168441433-T-G is Benign according to our data. Variant chr6-168441433-T-G is described in ClinVar as [Benign]. Clinvar id is 1257770.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.212 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMOC2 | NM_001166412.2 | c.63T>G | p.Ala21= | synonymous_variant | 1/13 | ENST00000356284.7 | |
SMOC2 | NM_022138.3 | c.63T>G | p.Ala21= | synonymous_variant | 1/13 | ||
SMOC2 | XM_011536065.2 | c.63T>G | p.Ala21= | synonymous_variant | 1/13 | ||
SMOC2 | XM_011536066.2 | c.63T>G | p.Ala21= | synonymous_variant | 1/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMOC2 | ENST00000356284.7 | c.63T>G | p.Ala21= | synonymous_variant | 1/13 | 1 | NM_001166412.2 | P3 | |
SMOC2 | ENST00000354536.9 | c.63T>G | p.Ala21= | synonymous_variant | 1/13 | 1 | A1 |
Frequencies
GnomAD3 genomes AF: 0.291 AC: 44154AN: 151866Hom.: 8315 Cov.: 33
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GnomAD3 exomes AF: 0.242 AC: 25101AN: 103790Hom.: 3873 AF XY: 0.242 AC XY: 13956AN XY: 57600
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GnomAD4 exome AF: 0.183 AC: 248438AN: 1355128Hom.: 28424 Cov.: 32 AF XY: 0.187 AC XY: 125250AN XY: 668024
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GnomAD4 genome AF: 0.291 AC: 44193AN: 151972Hom.: 8327 Cov.: 33 AF XY: 0.293 AC XY: 21756AN XY: 74258
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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