NM_004483.5:c.62C>T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004483.5(GCSH):c.62C>T(p.Ser21Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.797 in 149,294 control chromosomes in the GnomAD database, including 48,741 homozygotes. 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 Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_004483.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GCSH | NM_004483.5 | c.62C>T | p.Ser21Leu | missense_variant | Exon 1 of 5 | ENST00000315467.9 | NP_004474.2 | |
GCSH | XM_017023136.3 | c.62C>T | p.Ser21Leu | missense_variant | Exon 1 of 5 | XP_016878625.1 | ||
GCSH | NR_033249.2 | n.179C>T | non_coding_transcript_exon_variant | Exon 1 of 4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GCSH | ENST00000315467.9 | c.62C>T | p.Ser21Leu | missense_variant | Exon 1 of 5 | 1 | NM_004483.5 | ENSP00000319531.3 | ||
ENSG00000284512 | ENST00000640345.1 | c.62C>T | p.Ser21Leu | missense_variant | Exon 1 of 6 | 5 | ENSP00000492798.1 | |||
ENSG00000260643 | ENST00000564536.2 | c.62C>T | p.Ser21Leu | missense_variant | Exon 1 of 6 | 5 | ENSP00000491651.1 |
Frequencies
GnomAD3 genomes AF: 0.797 AC: 118919AN: 149186Hom.: 48732 Cov.: 34
GnomAD3 exomes AF: 0.540 AC: 696AN: 1288Hom.: 61 AF XY: 0.552 AC XY: 428AN XY: 776
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.642 AC: 671291AN: 1045944Hom.: 156214 Cov.: 32 AF XY: 0.647 AC XY: 327531AN XY: 506550
GnomAD4 genome AF: 0.797 AC: 118945AN: 149294Hom.: 48741 Cov.: 34 AF XY: 0.793 AC XY: 57799AN XY: 72908
ClinVar
Submissions by phenotype
Glycine encephalopathy Benign:2
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not provided Benign:2
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GCSH-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at