chrX-21967259-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_004595.5(SMS):c.113C>T(p.Ser38Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000448 in 1,205,657 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 19 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. S38S) has been classified as Likely benign.
Frequency
Consequence
NM_004595.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMS | NM_004595.5 | c.113C>T | p.Ser38Leu | missense_variant | 2/11 | ENST00000404933.7 | |
SMS | NM_001258423.2 | c.113C>T | p.Ser38Leu | missense_variant | 2/9 | ||
SMS | XM_005274582.3 | c.11C>T | p.Ser4Leu | missense_variant | 2/11 | ||
SMS | XM_011545568.3 | c.11C>T | p.Ser4Leu | missense_variant | 2/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMS | ENST00000404933.7 | c.113C>T | p.Ser38Leu | missense_variant | 2/11 | 1 | NM_004595.5 | P1 | |
SMS | ENST00000457085.2 | c.458C>T | p.Ser153Leu | missense_variant | 2/6 | 5 | |||
SMS | ENST00000379404.5 | c.113C>T | p.Ser38Leu | missense_variant | 2/9 | 3 | |||
SMS | ENST00000478094.1 | n.160C>T | non_coding_transcript_exon_variant | 2/5 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000456 AC: 5AN: 109538Hom.: 0 Cov.: 21 AF XY: 0.0000629 AC XY: 2AN XY: 31776
GnomAD3 exomes AF: 0.0000327 AC: 6AN: 183296Hom.: 0 AF XY: 0.0000443 AC XY: 3AN XY: 67758
GnomAD4 exome AF: 0.0000447 AC: 49AN: 1096119Hom.: 0 Cov.: 29 AF XY: 0.0000470 AC XY: 17AN XY: 361557
GnomAD4 genome AF: 0.0000456 AC: 5AN: 109538Hom.: 0 Cov.: 21 AF XY: 0.0000629 AC XY: 2AN XY: 31776
ClinVar
Submissions by phenotype
Syndromic X-linked intellectual disability Snyder type Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Apr 15, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at