rs78237438
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Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_001127217.3(SMAD9):c.12C>T(p.Thr4Thr) variant causes a synonymous change. The variant allele was found at a frequency of 0.00134 in 1,614,132 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0069 ( 9 hom., cov: 33)
Exomes 𝑓: 0.00076 ( 10 hom. )
Consequence
SMAD9
NM_001127217.3 synonymous
NM_001127217.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.73
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 -18 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
Variant 13-36879678-G-A is Benign according to our data. Variant chr13-36879678-G-A is described in ClinVar as [Benign]. Clinvar id is 227076.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00688 (1048/152318) while in subpopulation AFR AF= 0.0231 (962/41572). AF 95% confidence interval is 0.0219. There are 9 homozygotes in gnomad4. There are 488 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1048 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMAD9 | NM_001127217.3 | c.12C>T | p.Thr4Thr | synonymous_variant | 2/7 | ENST00000379826.5 | NP_001120689.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMAD9 | ENST00000379826.5 | c.12C>T | p.Thr4Thr | synonymous_variant | 2/7 | 5 | NM_001127217.3 | ENSP00000369154.4 | ||
SMAD9 | ENST00000350148.10 | c.12C>T | p.Thr4Thr | synonymous_variant | 2/6 | 1 | ENSP00000239885.6 | |||
SMAD9 | ENST00000399275.7 | n.12C>T | non_coding_transcript_exon_variant | 1/6 | 1 | ENSP00000382216.3 | ||||
SMAD9 | ENST00000483941.2 | n.451C>T | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00685 AC: 1042AN: 152200Hom.: 9 Cov.: 33
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GnomAD3 exomes AF: 0.00196 AC: 491AN: 250662Hom.: 3 AF XY: 0.00147 AC XY: 199AN XY: 135528
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GnomAD4 exome AF: 0.000759 AC: 1110AN: 1461814Hom.: 10 Cov.: 32 AF XY: 0.000670 AC XY: 487AN XY: 727206
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GnomAD4 genome AF: 0.00688 AC: 1048AN: 152318Hom.: 9 Cov.: 33 AF XY: 0.00655 AC XY: 488AN XY: 74484
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Pulmonary hypertension, primary, 2 Benign:2
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Dec 11, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 17, 2024 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 01, 2020 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Feb 21, 2013 | Thr4Thr in exon 2 of SMAD9: This variant is not expected to have clinical signif icance because it does not alter an amino acid residue and is not located within the splice consensus sequence. It has been identified in 2.7% (120/4406) of Afr ican American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS; dbSNP rs78237438). - |
Computational scores
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BayesDel_noAF
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