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GeneBe

3-12152585-T-C

Variant summary

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

The NM_133625.6(SYN2):c.774+1259T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.836 in 152,168 control chromosomes in the GnomAD database, including 53,596 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 0.84 ( 53596 hom., cov: 31)

Consequence

SYN2
NM_133625.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.41
Variant links:
Genes affected
SYN2 (HGNC:11495): (synapsin II) This gene is a member of the synapsin gene family. Synapsins encode neuronal phosphoproteins which associate with the cytoplasmic surface of synaptic vesicles. Family members are characterized by common protein domains, and they are implicated in synaptogenesis and the modulation of neurotransmitter release, suggesting a potential role in several neuropsychiatric diseases. This member of the synapsin family encodes a neuron-specific phosphoprotein that selectively binds to small synaptic vesicles in the presynaptic nerve terminal. Polymorphisms in this gene are associated with abnormal presynaptic function and related neuronal disorders, including autism, epilepsy, bipolar disorder and schizophrenia. Alternative splicing of this gene results in multiple transcript variants. The tissue inhibitor of metalloproteinase 4 gene is located within an intron of this gene and is transcribed in the opposite direction. [provided by RefSeq, Feb 2014]

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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=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SYN2NM_133625.6 linkuse as main transcriptc.774+1259T>C intron_variant ENST00000621198.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SYN2ENST00000621198.5 linkuse as main transcriptc.774+1259T>C intron_variant 1 NM_133625.6 P2Q92777-1
SYN2ENST00000620175.4 linkuse as main transcriptc.774+1259T>C intron_variant 1 A2Q92777-2
SYN2ENST00000439861.5 linkuse as main transcriptn.225+1259T>C intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.836
AC:
127136
AN:
152050
Hom.:
53556
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.728
Gnomad AMI
AF:
0.918
Gnomad AMR
AF:
0.895
Gnomad ASJ
AF:
0.908
Gnomad EAS
AF:
0.808
Gnomad SAS
AF:
0.906
Gnomad FIN
AF:
0.910
Gnomad MID
AF:
0.927
Gnomad NFE
AF:
0.868
Gnomad OTH
AF:
0.852
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.836
AC:
127226
AN:
152168
Hom.:
53596
Cov.:
31
AF XY:
0.841
AC XY:
62570
AN XY:
74404
show subpopulations
Gnomad4 AFR
AF:
0.728
Gnomad4 AMR
AF:
0.895
Gnomad4 ASJ
AF:
0.908
Gnomad4 EAS
AF:
0.808
Gnomad4 SAS
AF:
0.907
Gnomad4 FIN
AF:
0.910
Gnomad4 NFE
AF:
0.868
Gnomad4 OTH
AF:
0.853
Alfa
AF:
0.865
Hom.:
53066
Bravo
AF:
0.829
Asia WGS
AF:
0.880
AC:
3060
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
Cadd
Benign
0.025
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

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

Other links and lift over

dbSNP: rs99365; hg19: chr3-12194085; API