chr1-34905129-A-AC
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_001080418.3(DLGAP3):c.254dupG(p.Ser86fs) variant causes a frameshift change. The variant allele was found at a frequency of 0.0000725 in 1,559,274 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000079 ( 0 hom. )
Consequence
DLGAP3
NM_001080418.3 frameshift
NM_001080418.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.89
Publications
1 publications found
Genes affected
DLGAP3 (HGNC:30368): (DLG associated protein 3) Predicted to enable PDZ domain binding activity; molecular adaptor activity; and scaffold protein binding activity. Predicted to be involved in protein-containing complex assembly and regulation of postsynaptic neurotransmitter receptor activity. Predicted to be located in synapse. Predicted to be part of postsynaptic density. Predicted to be active in several cellular components, including cholinergic synapse; glutamatergic synapse; and neuromuscular junction. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 1-34905129-A-AC is Benign according to our data. Variant chr1-34905129-A-AC is described in ClinVar as [Likely_benign]. Clinvar id is 757628.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| DLGAP3 | NM_001080418.3 | c.254dupG | p.Ser86fs | frameshift_variant | Exon 3 of 12 | ENST00000373347.6 | NP_001073887.1 | |
| DLGAP3 | XM_011541879.3 | c.254dupG | p.Ser86fs | frameshift_variant | Exon 4 of 13 | XP_011540181.1 | ||
| DLGAP3 | XM_047426631.1 | c.254dupG | p.Ser86fs | frameshift_variant | Exon 3 of 12 | XP_047282587.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| DLGAP3 | ENST00000373347.6 | c.254dupG | p.Ser86fs | frameshift_variant | Exon 3 of 12 | 5 | NM_001080418.3 | ENSP00000362444.1 | ||
| DLGAP3 | ENST00000235180.4 | c.254dupG | p.Ser86fs | frameshift_variant | Exon 1 of 10 | 2 | ENSP00000235180.4 | |||
| DLGAP3 | ENST00000495979.1 | n.*35dupG | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes 0.0000135 AC: 2AN: 148224Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
148224
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:
GnomAD2 exomes AF: 0.000515 AC: 80AN: 155282 AF XY: 0.000167 show subpopulations
GnomAD2 exomes
AF:
AC:
80
AN:
155282
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000787 AC: 111AN: 1411050Hom.: 0 Cov.: 33 AF XY: 0.0000789 AC XY: 55AN XY: 697458 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
111
AN:
1411050
Hom.:
Cov.:
33
AF XY:
AC XY:
55
AN XY:
697458
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
32380
American (AMR)
AF:
AC:
4
AN:
37808
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25100
East Asian (EAS)
AF:
AC:
1
AN:
37146
South Asian (SAS)
AF:
AC:
4
AN:
80358
European-Finnish (FIN)
AF:
AC:
94
AN:
49404
Middle Eastern (MID)
AF:
AC:
0
AN:
5534
European-Non Finnish (NFE)
AF:
AC:
7
AN:
1084900
Other (OTH)
AF:
AC:
1
AN:
58420
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.271
Heterozygous variant carriers
0
13
26
38
51
64
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.0000135 AC: 2AN: 148224Hom.: 0 Cov.: 32 AF XY: 0.0000277 AC XY: 2AN XY: 72176 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
148224
Hom.:
Cov.:
32
AF XY:
AC XY:
2
AN XY:
72176
show subpopulations
African (AFR)
AF:
AC:
0
AN:
39902
American (AMR)
AF:
AC:
2
AN:
14954
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3426
East Asian (EAS)
AF:
AC:
0
AN:
5024
South Asian (SAS)
AF:
AC:
0
AN:
4646
European-Finnish (FIN)
AF:
AC:
0
AN:
10124
Middle Eastern (MID)
AF:
AC:
0
AN:
310
European-Non Finnish (NFE)
AF:
AC:
0
AN:
66892
Other (OTH)
AF:
AC:
0
AN:
2050
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jul 06, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
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
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.