rs11627546
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001034852.3(SMOC1):c.99+19430A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 152,114 control chromosomes in the GnomAD database, including 39,043 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.67 ( 39043 hom., cov: 32)
Consequence
SMOC1
NM_001034852.3 intron
NM_001034852.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0140
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMOC1 | NM_001034852.3 | c.99+19430A>C | intron_variant | ENST00000361956.8 | |||
SMOC1 | NM_022137.6 | c.99+19430A>C | intron_variant | ||||
SMOC1 | XM_005267995.2 | c.99+19430A>C | intron_variant | ||||
SMOC1 | XM_005267996.2 | c.99+19430A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMOC1 | ENST00000361956.8 | c.99+19430A>C | intron_variant | 1 | NM_001034852.3 | A2 | |||
SMOC1 | ENST00000381280.4 | c.99+19430A>C | intron_variant | 1 | P4 | ||||
SMOC1 | ENST00000555917.1 | n.404+34993A>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.672 AC: 102154AN: 151996Hom.: 39037 Cov.: 32
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.672 AC: 102187AN: 152114Hom.: 39043 Cov.: 32 AF XY: 0.679 AC XY: 50467AN XY: 74364
GnomAD4 genome
?
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50467
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2729
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
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