rs1787663

Positions:

• chr11-65527359-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020680.4(SCYL1):​c.849+242C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,080 control chromosomes in the GnomAD database, including 8,316 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.31 (8316 hom., cov: 31)
• Consequence: SCYL1 NM_020680.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.551

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCYL1	NM_020680.4	c.849+242C>A		intron_variant		ENST00000270176.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCYL1	ENST00000270176.10	c.849+242C>A		intron_variant		1	NM_020680.4	P1

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47498 AN: 151962 Hom.: 8300 Cov.: 31

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.274

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.313 AC: 47542 AN: 152080 Hom.: 8316 Cov.: 31 AF XY: 0.302 AC XY: 22426 AN XY: 74322

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.270

Alfa AF: 0.279 Hom.: 7904

Bravo AF: 0.331

Asia WGS AF: 0.241 AC: 838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs1787663; hg19: chr11-65294830;