1-169854470-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_020423.7(SCYL3):c.1807G>A(p.Glu603Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,613,962 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020423.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCYL3 | ENST00000367771.11 | c.1807G>A | p.Glu603Lys | missense_variant | Exon 12 of 13 | 1 | NM_020423.7 | ENSP00000356745.5 | ||
SCYL3 | ENST00000367770.5 | c.1969G>A | p.Glu657Lys | missense_variant | Exon 12 of 13 | 1 | ENSP00000356744.1 | |||
SCYL3 | ENST00000367772.8 | c.1969G>A | p.Glu657Lys | missense_variant | Exon 13 of 14 | 2 | ENSP00000356746.4 | |||
SCYL3 | ENST00000423670.1 | c.*41G>A | downstream_gene_variant | 5 | ENSP00000407993.1 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251296Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135850
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461820Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 727222
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1969G>A (p.E657K) alteration is located in exon 13 (coding exon 12) of the SCYL3 gene. This alteration results from a G to A substitution at nucleotide position 1969, causing the glutamic acid (E) at amino acid position 657 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at