chr6-168510073-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001166412.2(SMOC2):c.243A>G(p.Arg81=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000589 in 1,613,998 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 0.000033 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000062 ( 0 hom. )
Consequence
SMOC2
NM_001166412.2 synonymous
NM_001166412.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.181
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 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=-0.91).
BP6
?
Variant 6-168510073-A-G is Benign according to our data. Variant chr6-168510073-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2184418.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.181 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMOC2 | NM_001166412.2 | c.243A>G | p.Arg81= | synonymous_variant | 2/13 | ENST00000356284.7 | |
SMOC2 | NM_022138.3 | c.243A>G | p.Arg81= | synonymous_variant | 2/13 | ||
SMOC2 | XM_011536065.2 | c.243A>G | p.Arg81= | synonymous_variant | 2/13 | ||
SMOC2 | XM_011536066.2 | c.243A>G | p.Arg81= | synonymous_variant | 2/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMOC2 | ENST00000356284.7 | c.243A>G | p.Arg81= | synonymous_variant | 2/13 | 1 | NM_001166412.2 | P3 | |
SMOC2 | ENST00000354536.9 | c.243A>G | p.Arg81= | synonymous_variant | 2/13 | 1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152260Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251404Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135890
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GnomAD4 exome AF: 0.0000616 AC: 90AN: 1461738Hom.: 0 Cov.: 31 AF XY: 0.0000619 AC XY: 45AN XY: 727150
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GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152260Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74392
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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 | Invitae | Oct 04, 2023 | - - |
Computational scores
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Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at