1-34905129-AC-A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_001080418.3(DLGAP3):c.254delG(p.Gly85ValfsTer215) variant causes a frameshift change. The variant allele was found at a frequency of 0.0000376 in 1,409,656 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000038 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
DLGAP3
NM_001080418.3 frameshift
NM_001080418.3 frameshift
Scores
Not classified
Clinical Significance
Not reported in ClinVar
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.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| DLGAP3 | NM_001080418.3 | c.254delG | p.Gly85ValfsTer215 | frameshift_variant | Exon 3 of 12 | ENST00000373347.6 | NP_001073887.1 | |
| DLGAP3 | XM_011541879.3 | c.254delG | p.Gly85ValfsTer215 | frameshift_variant | Exon 4 of 13 | XP_011540181.1 | ||
| DLGAP3 | XM_047426631.1 | c.254delG | p.Gly85ValfsTer215 | 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.254delG | p.Gly85ValfsTer215 | frameshift_variant | Exon 3 of 12 | 5 | NM_001080418.3 | ENSP00000362444.1 | ||
| DLGAP3 | ENST00000235180.4 | c.254delG | p.Gly85ValfsTer215 | frameshift_variant | Exon 1 of 10 | 2 | ENSP00000235180.4 | |||
| DLGAP3 | ENST00000495979.1 | n.*35delG | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 148218Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
0
AN:
148218
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
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Gnomad EAS
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Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
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Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.000367 AC: 57AN: 155282 AF XY: 0.000382 show subpopulations
GnomAD2 exomes
AF:
AC:
57
AN:
155282
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
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GnomAD4 exome AF: 0.0000376 AC: 53AN: 1409656Hom.: 0 Cov.: 33 AF XY: 0.0000402 AC XY: 28AN XY: 696736 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
53
AN:
1409656
Hom.:
Cov.:
33
AF XY:
AC XY:
28
AN XY:
696736
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
1
AN:
32354
American (AMR)
AF:
AC:
9
AN:
37684
Ashkenazi Jewish (ASJ)
AF:
AC:
2
AN:
25056
East Asian (EAS)
AF:
AC:
1
AN:
37130
South Asian (SAS)
AF:
AC:
3
AN:
80234
European-Finnish (FIN)
AF:
AC:
1
AN:
49540
Middle Eastern (MID)
AF:
AC:
0
AN:
5528
European-Non Finnish (NFE)
AF:
AC:
33
AN:
1083778
Other (OTH)
AF:
AC:
3
AN:
58352
⚠️ 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: 0.251
Heterozygous variant carriers
0
9
17
26
34
43
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.00 AC: 0AN: 148320Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 72286
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
148320
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
72286
African (AFR)
AF:
AC:
0
AN:
40010
American (AMR)
AF:
AC:
0
AN:
14972
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3426
East Asian (EAS)
AF:
AC:
0
AN:
5012
South Asian (SAS)
AF:
AC:
0
AN:
4642
European-Finnish (FIN)
AF:
AC:
0
AN:
10124
Middle Eastern (MID)
AF:
AC:
0
AN:
290
European-Non Finnish (NFE)
AF:
AC:
0
AN:
66878
Other (OTH)
AF:
AC:
0
AN:
2070
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational 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
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