NM_005902.4:c.-2C>G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005902.4(SMAD3):c.-2C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000139 in 1,437,784 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 Uncertain significance (★).
Frequency
Consequence
NM_005902.4 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMAD3 | NM_005902.4 | c.-2C>G | 5_prime_UTR_variant | Exon 1 of 9 | ENST00000327367.9 | NP_005893.1 | ||
SMAD3 | NM_001407011.1 | c.-2C>G | 5_prime_UTR_variant | Exon 1 of 10 | NP_001393940.1 | |||
SMAD3 | NM_001407012.1 | c.-2C>G | 5_prime_UTR_variant | Exon 1 of 8 | NP_001393941.1 | |||
SMAD3 | NM_001407013.1 | c.-2C>G | 5_prime_UTR_variant | Exon 1 of 8 | NP_001393942.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMAD3 | ENST00000327367 | c.-2C>G | 5_prime_UTR_variant | Exon 1 of 9 | 1 | NM_005902.4 | ENSP00000332973.4 | |||
SMAD3 | ENST00000560424 | c.-2C>G | 5_prime_UTR_variant | Exon 1 of 10 | 3 | ENSP00000455540.2 | ||||
SMAD3 | ENST00000559460.6 | c.-110+2209C>G | intron_variant | Intron 1 of 8 | 4 | ENSP00000453082.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000476 AC: 1AN: 209868Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 113836
GnomAD4 exome AF: 0.00000139 AC: 2AN: 1437784Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 713136
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Familial thoracic aortic aneurysm and aortic dissection Uncertain:1
This variant changes 1 nucleotide in the 5' untranslated region of the SMAD3 gene. To our knowledge, functional studies have not been performed for this variant. This variant has not been reported in individuals affected with cardiovascular disorders in the literature. This variant has been identified in 1/209868 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at