rs10800485

Variant names:

• chr1-169878005-C-T
• rs10800485
• NM_020423.7:c.351+629G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020423.7(SCYL3):​c.351+629G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.722 in 152,078 control chromosomes in the GnomAD database, including 40,535 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 0.72 (40535 hom., cov: 31)
• Consequence: SCYL3 NM_020423.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 8 publications found

Genes affected

SCYL3 (HGNC:19285): (SCY1 like pseudokinase 3) This gene encodes a protein with a kinase domain and four HEAT repeats. The encoded protein interacts with the C-terminal domain of ezrin, an ERM protein, and may play a role in cell adhesion and migration. Alternative splicing results in multiple transcript variants encoding multiple isoforms. [provided by RefSeq, Jun 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCYL3	NM_020423.7	c.351+629G>A		intron_variant	Intron 3 of 12	ENST00000367771.11	NP_065156.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCYL3	ENST00000367771.11	c.351+629G>A		intron_variant	Intron 3 of 12	1	NM_020423.7	ENSP00000356745.5

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109748 AN: 151960 Hom.: 40487 Cov.: 31

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.722 AC: 109855 AN: 152078 Hom.: 40535 Cov.: 31 AF XY: 0.718 AC XY: 53363 AN XY: 74336

African (AFR) AF: 0.861 AC: 35741 AN: 41500

American (AMR) AF: 0.723 AC: 11038 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2737 AN: 3470

East Asian (EAS) AF: 0.444 AC: 2293 AN: 5168

South Asian (SAS) AF: 0.762 AC: 3676 AN: 4822

European-Finnish (FIN) AF: 0.595 AC: 6280 AN: 10554

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45633 AN: 67972

Other (OTH) AF: 0.724 AC: 1529 AN: 2112

Alfa AF: 0.699 Hom.: 63302

Bravo AF: 0.734

Asia WGS AF: 0.620 AC: 2156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.32
DANN	Benign	0.62
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10800485; hg19: chr1-169847146;