22-31089709-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_134269.3(SMTN):c.482G>A(p.Arg161Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000122 in 1,598,314 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_134269.3 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMTN | NM_134269.3 | c.482G>A | p.Arg161Gln | missense_variant | 7/21 | ENST00000333137.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMTN | ENST00000333137.12 | c.482G>A | p.Arg161Gln | missense_variant | 7/21 | 1 | NM_134269.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152144Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000125 AC: 30AN: 240886Hom.: 0 AF XY: 0.000115 AC XY: 15AN XY: 130922
GnomAD4 exome AF: 0.000123 AC: 178AN: 1446170Hom.: 0 Cov.: 33 AF XY: 0.000124 AC XY: 89AN XY: 718914
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152144Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 19, 2023 | The c.644G>A (p.R215Q) alteration is located in exon 7 (coding exon 7) of the SMTN gene. This alteration results from a G to A substitution at nucleotide position 644, causing the arginine (R) at amino acid position 215 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at