chr1-41028702-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001394311.1(SCMH1):c.1769G>T(p.Arg590Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000204 in 1,613,980 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R590H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001394311.1 missense
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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCMH1 | NM_001394311.1 | c.1769G>T | p.Arg590Leu | missense_variant | 15/16 | ENST00000695335.1 | NP_001381240.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCMH1 | ENST00000695335.1 | c.1769G>T | p.Arg590Leu | missense_variant | 15/16 | NM_001394311.1 | ENSP00000511813.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249264Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134924
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461838Hom.: 0 Cov.: 33 AF XY: 0.0000248 AC XY: 18AN XY: 727214
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 05, 2024 | The c.1739G>T (p.R580L) alteration is located in exon 15 (coding exon 12) of the SCMH1 gene. This alteration results from a G to T substitution at nucleotide position 1739, causing the arginine (R) at amino acid position 580 to be replaced by a leucine (L). 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