rs3764942
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000509297.6(SMAD5):c.-393C>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 0.0969 in 154,682 control chromosomes in the GnomAD database, including 869 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 0.097 ( 847 hom., cov: 32)
Exomes 𝑓: 0.12 ( 22 hom. )
Consequence
SMAD5
ENST00000509297.6 5_prime_UTR
ENST00000509297.6 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.779
Genes affected
SMAD5 (HGNC:6771): (SMAD family member 5) The protein encoded by this gene is involved in the transforming growth factor beta signaling pathway that results in an inhibition of the proliferation of hematopoietic progenitor cells. The encoded protein is activated by bone morphogenetic proteins type 1 receptor kinase, and may be involved in cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]
SMAD5-AS1 (HGNC:30586): (SMAD5 antisense RNA 1) Predicted to be involved in signal transduction. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.54).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMAD5 | NM_005903.7 | c.-245+849C>T | intron_variant | ENST00000545279.6 | |||
SMAD5-AS1 | NR_026763.1 | n.1080G>A | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMAD5 | ENST00000545279.6 | c.-245+849C>T | intron_variant | 1 | NM_005903.7 | P1 | |||
SMAD5-AS1 | ENST00000297163.3 | n.1080G>A | non_coding_transcript_exon_variant | 1/2 | 1 | ||||
ENST00000617906.1 | n.116C>T | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.0965 AC: 14657AN: 151920Hom.: 844 Cov.: 32
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GnomAD4 exome AF: 0.116 AC: 306AN: 2644Hom.: 22 Cov.: 0 AF XY: 0.105 AC XY: 142AN XY: 1358
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GnomAD4 genome AF: 0.0966 AC: 14683AN: 152038Hom.: 847 Cov.: 32 AF XY: 0.100 AC XY: 7456AN XY: 74302
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ClinVar
Not reported inComputational scores
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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