rs763869
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001346810.2(DLGAP2):c.107-73922G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 152,048 control chromosomes in the GnomAD database, including 21,016 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 0.52 ( 21016 hom., cov: 33)
Consequence
DLGAP2
NM_001346810.2 intron
NM_001346810.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.698
Publications
16 publications found
Genes affected
DLGAP2 (HGNC:2906): (DLG associated protein 2) The product of this gene is a membrane-associated protein that may play a role in synapse organization and signalling in neuronal cells. This gene is biallelically expressed in the brain, however, only the paternal allele is expressed in the testis (PMID:18055845). Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jun 2014]
DLGAP2 Gene-Disease associations (from GenCC):
- complex neurodevelopmental disorderInheritance: AD Classification: LIMITED Submitted by: ClinGen
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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=-1.0).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DLGAP2 | NM_001346810.2 | c.107-73922G>A | intron_variant | Intron 3 of 14 | ENST00000637795.2 | NP_001333739.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DLGAP2 | ENST00000637795.2 | c.107-73922G>A | intron_variant | Intron 3 of 14 | 5 | NM_001346810.2 | ENSP00000489774.1 | |||
DLGAP2 | ENST00000421627.7 | c.104-73922G>A | intron_variant | Intron 3 of 14 | 5 | ENSP00000400258.3 |
Frequencies
GnomAD3 genomes AF: 0.522 AC: 79256AN: 151930Hom.: 20980 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
79256
AN:
151930
Hom.:
Cov.:
33
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: 0.522 AC: 79343AN: 152048Hom.: 21016 Cov.: 33 AF XY: 0.528 AC XY: 39208AN XY: 74300 show subpopulations
GnomAD4 genome
AF:
AC:
79343
AN:
152048
Hom.:
Cov.:
33
AF XY:
AC XY:
39208
AN XY:
74300
show subpopulations
African (AFR)
AF:
AC:
20242
AN:
41472
American (AMR)
AF:
AC:
8949
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
AC:
1933
AN:
3466
East Asian (EAS)
AF:
AC:
3356
AN:
5176
South Asian (SAS)
AF:
AC:
3493
AN:
4820
European-Finnish (FIN)
AF:
AC:
5784
AN:
10568
Middle Eastern (MID)
AF:
AC:
146
AN:
294
European-Non Finnish (NFE)
AF:
AC:
33817
AN:
67960
Other (OTH)
AF:
AC:
1106
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1981
3963
5944
7926
9907
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
702
1404
2106
2808
3510
<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:
2250
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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