rs6990312

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001099754.2(SYBU):​c.428-3926C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 151,678 control chromosomes in the GnomAD database, including 10,292 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 0.29 ( 10292 hom., cov: 31)

Consequence

SYBU
NM_001099754.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.725
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SYBUNM_001099754.2 linkc.428-3926C>A intron_variant Intron 3 of 6 ENST00000276646.14 NP_001093224.1 Q9NX95-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SYBUENST00000276646.14 linkc.428-3926C>A intron_variant Intron 3 of 6 1 NM_001099754.2 ENSP00000276646.9 Q9NX95-1
SYBUENST00000424158.6 linkc.443-3926C>A intron_variant Intron 5 of 8 1 ENSP00000415654.2 A0A0C4DG86

Frequencies

GnomAD3 genomes
AF:
0.290
AC:
43930
AN:
151568
Hom.:
10239
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.638
Gnomad AMI
AF:
0.103
Gnomad AMR
AF:
0.266
Gnomad ASJ
AF:
0.176
Gnomad EAS
AF:
0.0125
Gnomad SAS
AF:
0.313
Gnomad FIN
AF:
0.100
Gnomad MID
AF:
0.278
Gnomad NFE
AF:
0.141
Gnomad OTH
AF:
0.289
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.290
AC:
44059
AN:
151678
Hom.:
10292
Cov.:
31
AF XY:
0.288
AC XY:
21372
AN XY:
74094
show subpopulations
Gnomad4 AFR
AF:
0.638
Gnomad4 AMR
AF:
0.267
Gnomad4 ASJ
AF:
0.176
Gnomad4 EAS
AF:
0.0124
Gnomad4 SAS
AF:
0.312
Gnomad4 FIN
AF:
0.100
Gnomad4 NFE
AF:
0.141
Gnomad4 OTH
AF:
0.298
Alfa
AF:
0.213
Hom.:
763
Bravo
AF:
0.314
Asia WGS
AF:
0.229
AC:
797
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
4.9
DANN
Benign
0.29

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

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

Other links and lift over

dbSNP: rs6990312; hg19: chr8-110602317; API