rs934648707
Positions:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001127217.3(SMAD9):c.603G>T(p.Pro201=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000109 in 1,461,862 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.000011 ( 0 hom. )
Consequence
SMAD9
NM_001127217.3 synonymous
NM_001127217.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.02
Genes affected
SMAD9 (HGNC:6774): (SMAD family member 9) The protein encoded by this gene is a member of the SMAD family, which transduces signals from TGF-beta family members. The encoded protein is activated by bone morphogenetic proteins and interacts with SMAD4. Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
?
Variant 13-36872725-C-A is Benign according to our data. Variant chr13-36872725-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 474935.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-4.02 with no splicing effect.
BS2
?
High AC in GnomAdExome4 at 16 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMAD9 | NM_001127217.3 | c.603G>T | p.Pro201= | synonymous_variant | 3/7 | ENST00000379826.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMAD9 | ENST00000379826.5 | c.603G>T | p.Pro201= | synonymous_variant | 3/7 | 5 | NM_001127217.3 | P1 | |
SMAD9 | ENST00000350148.10 | c.603G>T | p.Pro201= | synonymous_variant | 3/6 | 1 | |||
SMAD9 | ENST00000399275.7 | c.*313G>T | 3_prime_UTR_variant, NMD_transcript_variant | 3/6 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 genomes
?
Cov.:
31
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461862Hom.: 0 Cov.: 33 AF XY: 0.00000825 AC XY: 6AN XY: 727234
GnomAD4 exome
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16
AN:
1461862
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33
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AC XY:
6
AN XY:
727234
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GnomAD4 genome ? Cov.: 31
GnomAD4 genome
?
Cov.:
31
Bravo
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Pulmonary hypertension, primary, 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 06, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
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