1-169854690-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020423.7(SCYL3):āc.1587C>Gā(p.Asn529Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000799 in 1,614,000 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_020423.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCYL3 | ENST00000367771.11 | c.1587C>G | p.Asn529Lys | missense_variant | 12/13 | 1 | NM_020423.7 | ENSP00000356745.5 | ||
SCYL3 | ENST00000367770.5 | c.1749C>G | p.Asn583Lys | missense_variant | 12/13 | 1 | ENSP00000356744.1 | |||
SCYL3 | ENST00000367772.8 | c.1749C>G | p.Asn583Lys | missense_variant | 13/14 | 2 | ENSP00000356746.4 | |||
SCYL3 | ENST00000423670.1 | c.1587C>G | p.Asn529Lys | missense_variant | 12/12 | 5 | ENSP00000407993.1 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152110Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000478 AC: 12AN: 250942Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135600
GnomAD4 exome AF: 0.0000780 AC: 114AN: 1461772Hom.: 0 Cov.: 34 AF XY: 0.0000701 AC XY: 51AN XY: 727202
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152228Hom.: 1 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74422
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2023 | The c.1749C>G (p.N583K) alteration is located in exon 13 (coding exon 12) of the SCYL3 gene. This alteration results from a C to G substitution at nucleotide position 1749, causing the asparagine (N) at amino acid position 583 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