chr7-129189117-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005631.5(SMO):c.-35G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000733 in 1,203,812 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0034 ( 4 hom., cov: 32)
Exomes 𝑓: 0.00035 ( 5 hom. )
Consequence
SMO
NM_005631.5 5_prime_UTR
NM_005631.5 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0530
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant 7-129189117-G-T is Benign according to our data. Variant chr7-129189117-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 1207639.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00339 (515/151964) while in subpopulation AFR AF= 0.0116 (482/41526). AF 95% confidence interval is 0.0108. There are 4 homozygotes in gnomad4. There are 242 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 4 SM gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMO | NM_005631.5 | c.-35G>T | 5_prime_UTR_variant | 1/12 | ENST00000249373.8 | ||
SMO | XM_047420759.1 | c.-539G>T | 5_prime_UTR_variant | 1/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMO | ENST00000249373.8 | c.-35G>T | 5_prime_UTR_variant | 1/12 | 1 | NM_005631.5 | P1 | ||
SMO | ENST00000655644.1 | c.-35G>T | 5_prime_UTR_variant, NMD_transcript_variant | 1/12 |
Frequencies
GnomAD3 genomes ? AF: 0.00338 AC: 513AN: 151856Hom.: 4 Cov.: 32
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GnomAD4 exome AF: 0.000349 AC: 367AN: 1051848Hom.: 5 Cov.: 26 AF XY: 0.000346 AC XY: 172AN XY: 496414
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GnomAD4 genome ? AF: 0.00339 AC: 515AN: 151964Hom.: 4 Cov.: 32 AF XY: 0.00326 AC XY: 242AN XY: 74300
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 09, 2019 | - - |
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
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at