chr15-67066150-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005902.4(SMAD3):c.-5C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000315 in 1,586,672 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMAD3 | NM_005902.4 | c.-5C>A | 5_prime_UTR_variant | Exon 1 of 9 | ENST00000327367.9 | NP_005893.1 | ||
SMAD3 | NM_001407011.1 | c.-5C>A | 5_prime_UTR_variant | Exon 1 of 10 | NP_001393940.1 | |||
SMAD3 | NM_001407012.1 | c.-5C>A | 5_prime_UTR_variant | Exon 1 of 8 | NP_001393941.1 | |||
SMAD3 | NM_001407013.1 | c.-5C>A | 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.-5C>A | 5_prime_UTR_variant | Exon 1 of 9 | 1 | NM_005902.4 | ENSP00000332973.4 | |||
SMAD3 | ENST00000560424 | c.-5C>A | 5_prime_UTR_variant | Exon 1 of 10 | 3 | ENSP00000455540.2 | ||||
SMAD3 | ENST00000559460.6 | c.-110+2206C>A | intron_variant | Intron 1 of 8 | 4 | ENSP00000453082.2 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152012Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000279 AC: 4AN: 1434660Hom.: 0 Cov.: 32 AF XY: 0.00000422 AC XY: 3AN XY: 711350
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152012Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74242
ClinVar
Submissions by phenotype
Aneurysm-osteoarthritis syndrome Uncertain:1
This variant changes a single nucleotide in the 5' untranslated region of the SMAD3 gene. To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with SMAD3-related disorders in the literature. This variant has not been identified 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