NM_001099754.2:c.427+631T>C

Variant names:

• chr8-109618211-A-G
• rs1954713
• NM_001099754.2:c.427+631T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SYBU	NM_001099754.2	c.427+631T>C		intron_variant	Intron 3 of 6	ENST00000276646.14	NP_001093224.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SYBU	ENST00000276646.14	c.427+631T>C		intron_variant	Intron 3 of 6	1	NM_001099754.2	ENSP00000276646.9
SYBU	ENST00000424158.6	c.442+631T>C		intron_variant	Intron 5 of 8	1		ENSP00000415654.2

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

African (AFR) AF: 0.0209 AC: 868 AN: 41572

American (AMR) AF: 0.0920 AC: 1407 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0775 AC: 269 AN: 3472

East Asian (EAS) AF: 0.361 AC: 1870 AN: 5174

South Asian (SAS) AF: 0.121 AC: 586 AN: 4824

European-Finnish (FIN) AF: 0.141 AC: 1491 AN: 10594

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0999 AC: 6797 AN: 68014

Other (OTH) AF: 0.0863 AC: 182 AN: 2110

Alfa AF: 0.0830 Hom.: 385

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
PhyloP100		-0.54
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: rs1954713; hg19: chr8-110630440;