rs13179769
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005903.7(SMAD5):c.404-2685C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 151,736 control chromosomes in the GnomAD database, including 10,837 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 0.36 ( 10837 hom., cov: 31)
Consequence
SMAD5
NM_005903.7 intron
NM_005903.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.42
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]
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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=-1.03).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMAD5 | ENST00000545279.6 | c.404-2685C>A | intron_variant | 1 | NM_005903.7 | ENSP00000441954.2 | ||||
SMAD5 | ENST00000509297.6 | c.404-2685C>A | intron_variant | 1 | ENSP00000426696.2 | |||||
SMAD5 | ENST00000545620.5 | c.404-2685C>A | intron_variant | 5 | ENSP00000446474.2 | |||||
SMAD5 | ENST00000514777.1 | n.60-14263C>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.360 AC: 54639AN: 151618Hom.: 10808 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.361 AC: 54714AN: 151736Hom.: 10837 Cov.: 31 AF XY: 0.356 AC XY: 26418AN XY: 74152
GnomAD4 genome
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74152
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ClinVar
Not reported inComputational 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