rs1954713

chr8-109618211-A-Gchr8-109618211-A-T

Variant summary

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

The NM_001099754.2(SYBU):c.427+631T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0897 in 152,256 control chromosomes in the GnomAD database, including 955 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 0.090 (955 hom., cov: 32)
• Consequence: SYBU NM_001099754.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.538

Genes affected

SYBU (HGNC:26011): (syntabulin) Syntabulin/GOLSYN is part of a kinesin motor-adaptor complex that is critical for the anterograde axonal transport of active zone components and contributes to activity-dependent presynaptic assembly during neuronal development (Cai et al., 2007 [PubMed 17611281]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SYBU	NM_001099754.2	c.427+631T>C		intron_variant		ENST00000276646.14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYBU	ENST00000276646.14	c.427+631T>C		intron_variant		1	NM_001099754.2	A1

Frequencies

GnomAD3 genomes AF: 0.0898 AC: 13662 AN: 152138 Hom.: 956 Cov.: 32

Gnomad AFR AF: 0.0209

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.0923

Gnomad ASJ AF: 0.0775

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0999

Gnomad OTH AF: 0.0872

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

GnomAD4 genome AF: 0.0897 AC: 13653 AN: 152256 Hom.: 955 Cov.: 32 AF XY: 0.0934 AC XY: 6952 AN XY: 74424

Gnomad4 AFR AF: 0.0209

Gnomad4 AMR AF: 0.0920

Gnomad4 ASJ AF: 0.0775

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.0999

Gnomad4 OTH AF: 0.0863

Alfa AF: 0.0925 Hom.: 332

Bravo AF: 0.0855

Asia WGS AF: 0.219 AC: 760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.82
Dann	Benign	0.52

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: rs1954713; hg19: chr8-110630440;