chrX-21940837-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004595.5(SMS):c.13C>G(p.Arg5Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict 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. R5W) has been classified as Uncertain significance.
Frequency
Consequence
NM_004595.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMS | NM_004595.5 | c.13C>G | p.Arg5Gly | missense_variant | 1/11 | ENST00000404933.7 | |
SMS | NM_001258423.2 | c.13C>G | p.Arg5Gly | missense_variant | 1/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMS | ENST00000404933.7 | c.13C>G | p.Arg5Gly | missense_variant | 1/11 | 1 | NM_004595.5 | P1 | |
SMS | ENST00000379404.5 | c.13C>G | p.Arg5Gly | missense_variant | 1/9 | 3 | |||
SMS | ENST00000478094.1 | n.60C>G | non_coding_transcript_exon_variant | 1/5 | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 22
GnomAD4 exome Cov.: 27
GnomAD4 genome ? Cov.: 22
ClinVar
Submissions by phenotype
Syndromic X-linked intellectual disability Snyder type Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | May 03, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at