rs11846426
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001034852.3(SMOC1):c.1161C>T(p.Phe387=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00124 in 1,614,182 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0069 ( 9 hom., cov: 31)
Exomes 𝑓: 0.00065 ( 16 hom. )
Consequence
SMOC1
NM_001034852.3 synonymous
NM_001034852.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.29
Genes affected
SMOC1 (HGNC:20318): (SPARC related modular calcium binding 1) This gene encodes a multi-domain secreted protein that may have a critical role in ocular and limb development. Mutations in this gene are associated with microphthalmia and limb anomalies. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2011]
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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=-0.5).
BP6
?
Variant 14-70023317-C-T is Benign according to our data. Variant chr14-70023317-C-T is described in ClinVar as [Benign]. Clinvar id is 257187.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=1.29 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00689 (1049/152292) while in subpopulation AFR AF= 0.0235 (978/41556). AF 95% confidence interval is 0.0223. There are 9 homozygotes in gnomad4. There are 492 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMOC1 | NM_001034852.3 | c.1161C>T | p.Phe387= | synonymous_variant | 11/12 | ENST00000361956.8 | |
SMOC1 | NM_022137.6 | c.1161C>T | p.Phe387= | synonymous_variant | 11/12 | ||
SMOC1 | XM_005267995.2 | c.1194C>T | p.Phe398= | synonymous_variant | 11/12 | ||
SMOC1 | XM_005267996.2 | c.1194C>T | p.Phe398= | synonymous_variant | 11/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMOC1 | ENST00000361956.8 | c.1161C>T | p.Phe387= | synonymous_variant | 11/12 | 1 | NM_001034852.3 | A2 | |
SMOC1 | ENST00000381280.4 | c.1161C>T | p.Phe387= | synonymous_variant | 11/12 | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00687 AC: 1046AN: 152174Hom.: 9 Cov.: 31
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GnomAD3 exomes AF: 0.00169 AC: 424AN: 251392Hom.: 5 AF XY: 0.00139 AC XY: 189AN XY: 135854
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GnomAD4 exome AF: 0.000652 AC: 953AN: 1461890Hom.: 16 Cov.: 32 AF XY: 0.000606 AC XY: 441AN XY: 727246
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GnomAD4 genome ? AF: 0.00689 AC: 1049AN: 152292Hom.: 9 Cov.: 31 AF XY: 0.00661 AC XY: 492AN XY: 74468
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 12, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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