rs5997872
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000333137.12(SMTN):c.1676C>T(p.Ala559Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 1,613,820 control chromosomes in the GnomAD database, including 23,040 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
ENST00000333137.12 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMTN | NM_134269.3 | c.1676C>T | p.Ala559Val | missense_variant | 12/21 | ENST00000333137.12 | NP_599031.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMTN | ENST00000333137.12 | c.1676C>T | p.Ala559Val | missense_variant | 12/21 | 1 | NM_134269.3 | ENSP00000329532 | P1 |
Frequencies
GnomAD3 genomes AF: 0.159 AC: 24237AN: 152138Hom.: 2060 Cov.: 33
GnomAD3 exomes AF: 0.143 AC: 36028AN: 251244Hom.: 2885 AF XY: 0.145 AC XY: 19667AN XY: 135820
GnomAD4 exome AF: 0.166 AC: 242315AN: 1461564Hom.: 20981 Cov.: 35 AF XY: 0.165 AC XY: 120255AN XY: 727088
GnomAD4 genome AF: 0.159 AC: 24272AN: 152256Hom.: 2059 Cov.: 33 AF XY: 0.156 AC XY: 11579AN XY: 74456
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at