rs7162912
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The ENST00000327367.9(SMAD3):c.206+2610T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 151,992 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00011 ( 0 hom., cov: 30)
Consequence
SMAD3
ENST00000327367.9 intron
ENST00000327367.9 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0750
Genes affected
SMAD3 (HGNC:6769): (SMAD family member 3) The SMAD family of proteins are a group of intracellular signal transducer proteins similar to the gene products of the Drosophila gene 'mothers against decapentaplegic' (Mad) and the C. elegans gene Sma. The SMAD3 protein functions in the transforming growth factor-beta signaling pathway, and transmits signals from the cell surface to the nucleus, regulating gene activity and cell proliferation. This protein forms a complex with other SMAD proteins and binds DNA, functioning both as a transcription factor and tumor suppressor. Mutations in this gene are associated with aneurysms-osteoarthritis syndrome and Loeys-Dietz Syndrome 3. [provided by RefSeq, May 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BS2
High AC in GnomAd4 at 17 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMAD3 | NM_005902.4 | c.206+2610T>A | intron_variant | ENST00000327367.9 | NP_005893.1 | |||
SMAD3 | NM_001407011.1 | c.206+2610T>A | intron_variant | NP_001393940.1 | ||||
SMAD3 | NM_001407012.1 | c.206+2610T>A | intron_variant | NP_001393941.1 | ||||
SMAD3 | NM_001407013.1 | c.206+2610T>A | intron_variant | NP_001393942.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMAD3 | ENST00000327367.9 | c.206+2610T>A | intron_variant | 1 | NM_005902.4 | ENSP00000332973 | P1 | |||
SMAD3 | ENST00000559460.6 | c.-110+5026T>A | intron_variant | 4 | ENSP00000453082 | |||||
SMAD3 | ENST00000560424.2 | c.206+2610T>A | intron_variant | 3 | ENSP00000455540 | |||||
SMAD3 | ENST00000679624.1 | c.-110+1057T>A | intron_variant | ENSP00000505445 |
Frequencies
GnomAD3 genomes AF: 0.0000856 AC: 13AN: 151870Hom.: 0 Cov.: 30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.000112 AC: 17AN: 151992Hom.: 0 Cov.: 30 AF XY: 0.000148 AC XY: 11AN XY: 74272
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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