chr11-65525203-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020680.4(SCYL1):c.50T>C(p.Ile17Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. I17I) has been classified as Likely benign.
Frequency
Consequence
NM_020680.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCYL1 | NM_020680.4 | c.50T>C | p.Ile17Thr | missense_variant | 1/18 | ENST00000270176.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCYL1 | ENST00000270176.10 | c.50T>C | p.Ile17Thr | missense_variant | 1/18 | 1 | NM_020680.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 30
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1307202Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 642618
GnomAD4 genome ? Cov.: 30
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 17, 2023 | The c.50T>C (p.I17T) alteration is located in exon 1 (coding exon 1) of the SCYL1 gene. This alteration results from a T to C substitution at nucleotide position 50, causing the isoleucine (I) at amino acid position 17 to be replaced by a threonine (T). 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
Publications
No publications associated with this variant yet.