chr5-156757598-G-T
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PM5PP3_Strong
The NM_000337.6(SGCD):c.593G>T(p.Arg198Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,457,160 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. R198Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_000337.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SGCD | NM_000337.6 | c.593G>T | p.Arg198Leu | missense_variant | 8/9 | ENST00000337851.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SGCD | ENST00000337851.9 | c.593G>T | p.Arg198Leu | missense_variant | 8/9 | 1 | NM_000337.6 | P4 | |
SGCD | ENST00000435422.7 | c.590G>T | p.Arg197Leu | missense_variant | 7/8 | 1 | A1 | ||
SGCD | ENST00000517913.5 | c.593G>T | p.Arg198Leu | missense_variant | 10/10 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000409 AC: 1AN: 244436Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132386
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1457160Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 724510
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at