chr3-63368874-C-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001130003.2(SYNPR):c.84+90132C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,168 control chromosomes in the GnomAD database, including 2,108 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 0.13 ( 2108 hom., cov: 32)
Consequence
SYNPR
NM_001130003.2 intron
NM_001130003.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.453
Publications
1 publications found
Genes affected
SYNPR (HGNC:16507): (synaptoporin) Predicted to be located in neuron projection and synaptic vesicle. Predicted to be integral component of membrane. Predicted to be active in synaptic vesicle membrane. Predicted to be integral component of synaptic vesicle membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
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 = 0.54 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SYNPR | NM_001130003.2 | c.84+90132C>G | intron_variant | Intron 2 of 5 | ENST00000478300.6 | NP_001123475.1 | ||
SYNPR | XM_017005731.1 | c.133-111958C>G | intron_variant | Intron 2 of 5 | XP_016861220.1 | |||
SYNPR | XM_017005732.3 | c.84+90132C>G | intron_variant | Intron 2 of 5 | XP_016861221.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.134 AC: 20424AN: 152050Hom.: 2104 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
20424
AN:
152050
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.134 AC: 20430AN: 152168Hom.: 2108 Cov.: 32 AF XY: 0.138 AC XY: 10279AN XY: 74370 show subpopulations
GnomAD4 genome
AF:
AC:
20430
AN:
152168
Hom.:
Cov.:
32
AF XY:
AC XY:
10279
AN XY:
74370
show subpopulations
African (AFR)
AF:
AC:
1542
AN:
41560
American (AMR)
AF:
AC:
2767
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
AC:
635
AN:
3470
East Asian (EAS)
AF:
AC:
2871
AN:
5150
South Asian (SAS)
AF:
AC:
1037
AN:
4816
European-Finnish (FIN)
AF:
AC:
1241
AN:
10582
Middle Eastern (MID)
AF:
AC:
34
AN:
294
European-Non Finnish (NFE)
AF:
AC:
9817
AN:
68002
Other (OTH)
AF:
AC:
345
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
840
1681
2521
3362
4202
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
230
460
690
920
1150
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1283
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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