7-129203141-G-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005631.5(SMO):c.332-243G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00372 in 152,292 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0037 ( 4 hom., cov: 32)
Consequence
SMO
NM_005631.5 intron
NM_005631.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.392
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 7-129203141-G-T is Benign according to our data. Variant chr7-129203141-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 1189668.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00372 (567/152292) while in subpopulation AFR AF= 0.0128 (533/41546). AF 95% confidence interval is 0.0119. There are 4 homozygotes in gnomad4. There are 268 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 4 SM gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMO | NM_005631.5 | c.332-243G>T | intron_variant | ENST00000249373.8 | |||
SMO | XM_047420759.1 | c.-59-243G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMO | ENST00000249373.8 | c.332-243G>T | intron_variant | 1 | NM_005631.5 | P1 | |||
SMO | ENST00000655644.1 | c.*196-243G>T | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00367 AC: 559AN: 152174Hom.: 4 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.00372 AC: 567AN: 152292Hom.: 4 Cov.: 32 AF XY: 0.00360 AC XY: 268AN XY: 74462
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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 | Feb 28, 2019 | - - |
Computational scores
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Name
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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