6-168526769-T-C
Variant names:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001166412.2(SMOC2):c.363+317T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 152,016 control chromosomes in the GnomAD database, including 37,420 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.68 ( 37420 hom., cov: 32)
Consequence
SMOC2
NM_001166412.2 intron
NM_001166412.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.48
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 6-168526769-T-C is Benign according to our data. Variant chr6-168526769-T-C is described in ClinVar as [Benign]. Clinvar id is 1253369.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMOC2 | NM_001166412.2 | c.363+317T>C | intron_variant | Intron 3 of 12 | ENST00000356284.7 | NP_001159884.1 | ||
SMOC2 | NM_022138.3 | c.363+317T>C | intron_variant | Intron 3 of 12 | NP_071421.1 | |||
SMOC2 | XM_011536065.2 | c.363+317T>C | intron_variant | Intron 3 of 12 | XP_011534367.1 | |||
SMOC2 | XM_011536066.2 | c.363+317T>C | intron_variant | Intron 3 of 12 | XP_011534368.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.681 AC: 103481AN: 151898Hom.: 37402 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.681 AC: 103543AN: 152016Hom.: 37420 Cov.: 32 AF XY: 0.685 AC XY: 50858AN XY: 74294
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jun 19, 2021
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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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