chr7-129206487-G-C
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_005631.5(SMO):āc.1164G>Cā(p.Gly388=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 1,613,838 control chromosomes in the GnomAD database, including 546,321 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.79 ( 47490 hom., cov: 31)
Exomes š: 0.83 ( 498831 hom. )
Consequence
SMO
NM_005631.5 synonymous
NM_005631.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.17
Genes affected
SMO (HGNC:11119): (smoothened, frizzled class receptor) The protein encoded by this gene is a G protein-coupled receptor that interacts with the patched protein, a receptor for hedgehog proteins. The encoded protein tranduces signals to other proteins after activation by a hedgehog protein/patched protein complex. [provided by RefSeq, Jul 2010]
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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=-0.47).
BP6
Variant 7-129206487-G-C is Benign according to our data. Variant chr7-129206487-G-C is described in ClinVar as [Benign]. Clinvar id is 403462.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=1.16 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMO | NM_005631.5 | c.1164G>C | p.Gly388= | synonymous_variant | 6/12 | ENST00000249373.8 | |
SMO | XM_047420759.1 | c.774G>C | p.Gly258= | synonymous_variant | 7/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMO | ENST00000249373.8 | c.1164G>C | p.Gly388= | synonymous_variant | 6/12 | 1 | NM_005631.5 | P1 | |
SMO | ENST00000495998.1 | n.109G>C | non_coding_transcript_exon_variant | 2/3 | 3 | ||||
SMO | ENST00000462420.2 | c.246G>C | p.Gly82= | synonymous_variant, NMD_transcript_variant | 2/5 | 4 | |||
SMO | ENST00000655644.1 | c.*1028G>C | 3_prime_UTR_variant, NMD_transcript_variant | 7/12 |
Frequencies
GnomAD3 genomes AF: 0.787 AC: 119557AN: 151978Hom.: 47468 Cov.: 31
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GnomAD3 exomes AF: 0.798 AC: 200632AN: 251400Hom.: 80651 AF XY: 0.803 AC XY: 109062AN XY: 135864
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GnomAD4 exome AF: 0.825 AC: 1205966AN: 1461742Hom.: 498831 Cov.: 57 AF XY: 0.825 AC XY: 599792AN XY: 727158
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GnomAD4 genome AF: 0.787 AC: 119629AN: 152096Hom.: 47490 Cov.: 31 AF XY: 0.783 AC XY: 58254AN XY: 74354
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Hamartoma of hypothalamus Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 14, 2019 | - - |
Computational scores
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BayesDel_noAF
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CADD
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DANN
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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