GeneBe

22-20861118-G-GTTTTT

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_004782.4(SNAP29):​c.237+1785_237+1789dupTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000033 ( 0 hom., cov: 0)

Consequence

SNAP29
NM_004782.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.487

Publications

0 publications found
Variant links:
Genes affected
SNAP29 (HGNC:11133): (synaptosome associated protein 29) This gene, a member of the SNAP25 gene family, encodes a protein involved in multiple membrane trafficking steps. Two other members of this gene family, SNAP23 and SNAP25, encode proteins that bind a syntaxin protein and mediate synaptic vesicle membrane docking and fusion to the plasma membrane. The protein encoded by this gene binds tightly to multiple syntaxins and is localized to intracellular membrane structures rather than to the plasma membrane. While the protein is mostly membrane-bound, a significant fraction of it is found free in the cytoplasm. Use of multiple polyadenylation sites has been noted for this gene. [provided by RefSeq, Jul 2008]
SNAP29 Gene-Disease associations (from GenCC):
  • CEDNIK syndrome
    Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: PanelApp Australia, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), G2P, Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SNAP29NM_004782.4 linkc.237+1785_237+1789dupTTTTT intron_variant Intron 1 of 4 ENST00000215730.12 NP_004773.1 O95721

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SNAP29ENST00000215730.12 linkc.237+1771_237+1772insTTTTT intron_variant Intron 1 of 4 1 NM_004782.4 ENSP00000215730.6 O95721
SNAP29ENST00000439214.1 linkc.-43+1478_-43+1479insTTTTT intron_variant Intron 1 of 4 3 ENSP00000411095.1 C9JAF7
SNAP29ENST00000490458.1 linkn.267+1771_267+1772insTTTTT intron_variant Intron 1 of 1 2

Frequencies

GnomAD3 genomes
AF:
0.0000328
AC:
4
AN:
121814
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000324
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000272
Gnomad FIN
AF:
0.000178
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000165
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0000328
AC:
4
AN:
121814
Hom.:
0
Cov.:
0
AF XY:
0.0000348
AC XY:
2
AN XY:
57486
show subpopulations
African (AFR)
AF:
0.0000323
AC:
1
AN:
30922
American (AMR)
AF:
0.00
AC:
0
AN:
11370
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3230
East Asian (EAS)
AF:
0.00
AC:
0
AN:
3894
South Asian (SAS)
AF:
0.000273
AC:
1
AN:
3660
European-Finnish (FIN)
AF:
0.000178
AC:
1
AN:
5612
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
212
European-Non Finnish (NFE)
AF:
0.0000165
AC:
1
AN:
60436
Other (OTH)
AF:
0.00
AC:
0
AN:
1636
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.438
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs362237; hg19: chr22-21215406; API