rs1268463

Variant summary

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

The NM_005639.3(SYT1):​c.166+32029T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 152,104 control chromosomes in the GnomAD database, including 38,900 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 0.71 ( 38900 hom., cov: 31)

Consequence

SYT1
NM_005639.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.168
Variant links:
Genes affected
SYT1 (HGNC:11509): (synaptotagmin 1) This gene encodes a member of the synaptotagmin protein family. The synaptotagmins are integral membrane proteins of synaptic vesicles that serve as calcium sensors in the process of vesicular trafficking and exocytosis. The encoded protein participates in triggering neurotransmitter release at the synapse in response to calcium binding. Mutations in this gene are associated with Baker-Gordon syndrome. [provided by RefSeq, Jan 2023]

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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=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SYT1NM_005639.3 linkuse as main transcriptc.166+32029T>G intron_variant ENST00000261205.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SYT1ENST00000261205.9 linkuse as main transcriptc.166+32029T>G intron_variant 1 NM_005639.3 P3

Frequencies

GnomAD3 genomes
AF:
0.710
AC:
107984
AN:
151986
Hom.:
38883
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.795
Gnomad AMI
AF:
0.860
Gnomad AMR
AF:
0.730
Gnomad ASJ
AF:
0.621
Gnomad EAS
AF:
0.416
Gnomad SAS
AF:
0.543
Gnomad FIN
AF:
0.728
Gnomad MID
AF:
0.636
Gnomad NFE
AF:
0.690
Gnomad OTH
AF:
0.693
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.710
AC:
108039
AN:
152104
Hom.:
38900
Cov.:
31
AF XY:
0.706
AC XY:
52522
AN XY:
74348
show subpopulations
Gnomad4 AFR
AF:
0.794
Gnomad4 AMR
AF:
0.730
Gnomad4 ASJ
AF:
0.621
Gnomad4 EAS
AF:
0.416
Gnomad4 SAS
AF:
0.542
Gnomad4 FIN
AF:
0.728
Gnomad4 NFE
AF:
0.690
Gnomad4 OTH
AF:
0.685
Alfa
AF:
0.689
Hom.:
47669
Bravo
AF:
0.718
Asia WGS
AF:
0.488
AC:
1698
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
1.4
DANN
Benign
0.58

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: rs1268463; hg19: chr12-79643494; API