NM_004483.5:c.53C>A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_004483.5(GCSH):c.53C>A(p.Ala18Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A18V) has been classified as Benign.
Frequency
Consequence
NM_004483.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GCSH | NM_004483.5 | c.53C>A | p.Ala18Glu | missense_variant | Exon 1 of 5 | ENST00000315467.9 | NP_004474.2 | |
GCSH | XM_017023136.3 | c.53C>A | p.Ala18Glu | missense_variant | Exon 1 of 5 | XP_016878625.1 | ||
GCSH | NR_033249.2 | n.170C>A | 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.53C>A | p.Ala18Glu | missense_variant | Exon 1 of 5 | 1 | NM_004483.5 | ENSP00000319531.3 | ||
ENSG00000284512 | ENST00000640345.1 | c.53C>A | p.Ala18Glu | missense_variant | Exon 1 of 6 | 5 | ENSP00000492798.1 | |||
ENSG00000260643 | ENST00000564536.2 | c.53C>A | p.Ala18Glu | missense_variant | Exon 1 of 6 | 5 | ENSP00000491651.1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152032Hom.: 0 Cov.: 33 FAILED QC
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 8.60e-7 AC: 1AN: 1162466Hom.: 0 Cov.: 27 AF XY: 0.00000178 AC XY: 1AN XY: 562860
GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 152032Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74266
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at