chr6-168441430-C-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_001166412.2(SMOC2):c.60C>G(p.Pro20=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000162 in 1,510,432 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 0.00016 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00016 ( 0 hom. )
Consequence
SMOC2
NM_001166412.2 synonymous
NM_001166412.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.406
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
?
Variant 6-168441430-C-G is Benign according to our data. Variant chr6-168441430-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 2075464.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.406 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMOC2 | NM_001166412.2 | c.60C>G | p.Pro20= | synonymous_variant | 1/13 | ENST00000356284.7 | |
SMOC2 | NM_022138.3 | c.60C>G | p.Pro20= | synonymous_variant | 1/13 | ||
SMOC2 | XM_011536065.2 | c.60C>G | p.Pro20= | synonymous_variant | 1/13 | ||
SMOC2 | XM_011536066.2 | c.60C>G | p.Pro20= | synonymous_variant | 1/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMOC2 | ENST00000356284.7 | c.60C>G | p.Pro20= | synonymous_variant | 1/13 | 1 | NM_001166412.2 | P3 | |
SMOC2 | ENST00000354536.9 | c.60C>G | p.Pro20= | synonymous_variant | 1/13 | 1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 152136Hom.: 0 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
24
AN:
152136
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000217 AC: 23AN: 105830Hom.: 0 AF XY: 0.000137 AC XY: 8AN XY: 58592
GnomAD3 exomes
AF:
AC:
23
AN:
105830
Hom.:
AF XY:
AC XY:
8
AN XY:
58592
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000162 AC: 220AN: 1358188Hom.: 0 Cov.: 32 AF XY: 0.000158 AC XY: 106AN XY: 669596
GnomAD4 exome
AF:
AC:
220
AN:
1358188
Hom.:
Cov.:
32
AF XY:
AC XY:
106
AN XY:
669596
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.000158 AC: 24AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74424
GnomAD4 genome
?
AF:
AC:
24
AN:
152244
Hom.:
Cov.:
33
AF XY:
AC XY:
11
AN XY:
74424
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 29, 2022 | - - |
SMOC2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 11, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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