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GeneBe

11-65525992-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_020680.4(SCYL1):c.324G>A(p.Glu108=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0226 in 1,613,410 control chromosomes in the GnomAD database, including 556 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.015 ( 28 hom., cov: 31)
Exomes 𝑓: 0.023 ( 528 hom. )

Consequence

SCYL1
NM_020680.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.507
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-65525992-G-A is Benign according to our data. Variant chr11-65525992-G-A is described in ClinVar as [Benign]. Clinvar id is 2121003.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.507 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0147 (2240/152314) while in subpopulation NFE AF= 0.0249 (1691/68020). AF 95% confidence interval is 0.0239. There are 28 homozygotes in gnomad4. There are 1000 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 28 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SCYL1NM_020680.4 linkuse as main transcriptc.324G>A p.Glu108= synonymous_variant 3/18 ENST00000270176.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SCYL1ENST00000270176.10 linkuse as main transcriptc.324G>A p.Glu108= synonymous_variant 3/181 NM_020680.4 P1Q96KG9-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0147
AC:
2240
AN:
152196
Hom.:
28
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00499
Gnomad AMI
AF:
0.0274
Gnomad AMR
AF:
0.0130
Gnomad ASJ
AF:
0.00317
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00124
Gnomad FIN
AF:
0.00744
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0248
Gnomad OTH
AF:
0.0100
GnomAD3 exomes
AF:
0.0138
AC:
3423
AN:
248914
Hom.:
48
AF XY:
0.0132
AC XY:
1789
AN XY:
135240
show subpopulations
Gnomad AFR exome
AF:
0.00486
Gnomad AMR exome
AF:
0.0116
Gnomad ASJ exome
AF:
0.00428
Gnomad EAS exome
AF:
0.0000557
Gnomad SAS exome
AF:
0.000882
Gnomad FIN exome
AF:
0.00687
Gnomad NFE exome
AF:
0.0233
Gnomad OTH exome
AF:
0.0172
GnomAD4 exome
AF:
0.0235
AC:
34282
AN:
1461096
Hom.:
528
Cov.:
33
AF XY:
0.0227
AC XY:
16512
AN XY:
726862
show subpopulations
Gnomad4 AFR exome
AF:
0.00326
Gnomad4 AMR exome
AF:
0.0117
Gnomad4 ASJ exome
AF:
0.00436
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00116
Gnomad4 FIN exome
AF:
0.00686
Gnomad4 NFE exome
AF:
0.0286
Gnomad4 OTH exome
AF:
0.0211
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0147
AC:
2240
AN:
152314
Hom.:
28
Cov.:
31
AF XY:
0.0134
AC XY:
1000
AN XY:
74470
show subpopulations
Gnomad4 AFR
AF:
0.00498
Gnomad4 AMR
AF:
0.0129
Gnomad4 ASJ
AF:
0.00317
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00124
Gnomad4 FIN
AF:
0.00744
Gnomad4 NFE
AF:
0.0249
Gnomad4 OTH
AF:
0.00993
Alfa
AF:
0.0200
Hom.:
37
Bravo
AF:
0.0148
Asia WGS
AF:
0.00260
AC:
9
AN:
3478
EpiCase
AF:
0.0230
EpiControl
AF:
0.0223

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJan 26, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.58
Cadd
Benign
7.3
Dann
Benign
0.52
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs55662663; hg19: chr11-65293463; API