NM_020423.7:c.1860T>C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_020423.7(SCYL3):c.1860T>C(p.Asp620Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,613,960 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 Likely benign (★).
Frequency
Consequence
NM_020423.7 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCYL3 | ENST00000367771.11 | c.1860T>C | p.Asp620Asp | synonymous_variant | Exon 12 of 13 | 1 | NM_020423.7 | ENSP00000356745.5 | ||
SCYL3 | ENST00000367770.5 | c.2022T>C | p.Asp674Asp | synonymous_variant | Exon 12 of 13 | 1 | ENSP00000356744.1 | |||
SCYL3 | ENST00000367772.8 | c.2022T>C | p.Asp674Asp | synonymous_variant | Exon 13 of 14 | 2 | ENSP00000356746.4 | |||
SCYL3 | ENST00000423670.1 | c.*94T>C | downstream_gene_variant | 5 | ENSP00000407993.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251208Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135806
GnomAD4 exome AF: 0.0000376 AC: 55AN: 1461814Hom.: 0 Cov.: 30 AF XY: 0.0000454 AC XY: 33AN XY: 727208
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152146Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74322
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at