rs3824
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005631.5(SMO):c.*561C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 261,698 control chromosomes in the GnomAD database, including 2,803 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 0.14 ( 1580 hom., cov: 32)
Exomes 𝑓: 0.14 ( 1223 hom. )
Consequence
SMO
NM_005631.5 3_prime_UTR
NM_005631.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.146
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMO | NM_005631.5 | c.*561C>G | 3_prime_UTR_variant | 12/12 | ENST00000249373.8 | ||
SMO | XM_047420759.1 | c.*561C>G | 3_prime_UTR_variant | 13/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMO | ENST00000249373.8 | c.*561C>G | 3_prime_UTR_variant | 12/12 | 1 | NM_005631.5 | P1 | ||
ENST00000466717.1 | n.129+405G>C | intron_variant, non_coding_transcript_variant | 3 | ||||||
SMO | ENST00000655644.1 | c.*2680C>G | 3_prime_UTR_variant, NMD_transcript_variant | 12/12 |
Frequencies
GnomAD3 genomes ? AF: 0.140 AC: 21246AN: 152076Hom.: 1570 Cov.: 32
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GnomAD4 exome AF: 0.139 AC: 15267AN: 109504Hom.: 1223 Cov.: 0 AF XY: 0.138 AC XY: 7219AN XY: 52198
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GnomAD4 genome ? AF: 0.140 AC: 21282AN: 152194Hom.: 1580 Cov.: 32 AF XY: 0.144 AC XY: 10696AN XY: 74414
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at