chr11-65526132-C-T
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 2P and 15B. PM2BP4_ModerateBP6_Very_StrongBP7BS1
The NM_020680.4(SCYL1):c.384C>T(p.Leu128=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,613,024 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
Genomes: 𝑓 0.000085 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
SCYL1
NM_020680.4 synonymous
NM_020680.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.455
Genes affected
SCYL1 (HGNC:14372): (SCY1 like pseudokinase 1) This gene encodes a transcriptional regulator belonging to the SCY1-like family of kinase-like proteins. The protein has a divergent N-terminal kinase domain that is thought to be catalytically inactive, and can bind specific DNA sequences through its C-terminal domain. It activates transcription of the telomerase reverse transcriptase and DNA polymerase beta genes. The protein has been localized to the nucleus, and also to the cytoplasm and centrosomes during mitosis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
Variant 11-65526132-C-T is Benign according to our data. Variant chr11-65526132-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2185611.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.455 with no splicing effect.
BS1
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00011 (160/1460746) while in subpopulation MID AF= 0.00156 (9/5766). AF 95% confidence interval is 0.000814. There are 0 homozygotes in gnomad4_exome. There are 81 alleles in male gnomad4_exome subpopulation. Median coverage is 33. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCYL1 | NM_020680.4 | c.384C>T | p.Leu128= | synonymous_variant | 4/18 | ENST00000270176.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCYL1 | ENST00000270176.10 | c.384C>T | p.Leu128= | synonymous_variant | 4/18 | 1 | NM_020680.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152160Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000154 AC: 38AN: 247394Hom.: 0 AF XY: 0.000156 AC XY: 21AN XY: 134778
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GnomAD4 exome AF: 0.000110 AC: 160AN: 1460746Hom.: 0 Cov.: 33 AF XY: 0.000111 AC XY: 81AN XY: 726692
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GnomAD4 genome AF: 0.0000854 AC: 13AN: 152278Hom.: 0 Cov.: 31 AF XY: 0.0000940 AC XY: 7AN XY: 74458
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
SCYL1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 21, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 07, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at