1-34904382-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_001080418.3(DLGAP3):c.1002C>T(p.Thr334Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000514 in 1,613,732 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0029 ( 5 hom., cov: 32)
Exomes 𝑓: 0.00026 ( 3 hom. )
Consequence
DLGAP3
NM_001080418.3 synonymous
NM_001080418.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.01
Publications
0 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: Benign. The variant received -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP6
Variant 1-34904382-G-A is Benign according to our data. Variant chr1-34904382-G-A is described in ClinVar as [Benign]. Clinvar id is 709546.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=3.01 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 5 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DLGAP3 | NM_001080418.3 | c.1002C>T | p.Thr334Thr | synonymous_variant | Exon 3 of 12 | ENST00000373347.6 | NP_001073887.1 | |
DLGAP3 | XM_011541879.3 | c.1002C>T | p.Thr334Thr | synonymous_variant | Exon 4 of 13 | XP_011540181.1 | ||
DLGAP3 | XM_047426631.1 | c.1002C>T | p.Thr334Thr | synonymous_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.1002C>T | p.Thr334Thr | synonymous_variant | Exon 3 of 12 | 5 | NM_001080418.3 | ENSP00000362444.1 | ||
DLGAP3 | ENST00000235180.4 | c.1002C>T | p.Thr334Thr | synonymous_variant | Exon 1 of 10 | 2 | ENSP00000235180.4 |
Frequencies
GnomAD3 genomes AF: 0.00293 AC: 446AN: 152226Hom.: 5 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
446
AN:
152226
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
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Gnomad ASJ
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AF:
Gnomad FIN
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Gnomad MID
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Gnomad NFE
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Gnomad OTH
AF:
GnomAD2 exomes AF: 0.000659 AC: 165AN: 250230 AF XY: 0.000479 show subpopulations
GnomAD2 exomes
AF:
AC:
165
AN:
250230
AF XY:
Gnomad AFR exome
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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: 0.000262 AC: 383AN: 1461388Hom.: 3 Cov.: 32 AF XY: 0.000221 AC XY: 161AN XY: 727044 show subpopulations
GnomAD4 exome
AF:
AC:
383
AN:
1461388
Hom.:
Cov.:
32
AF XY:
AC XY:
161
AN XY:
727044
show subpopulations
African (AFR)
AF:
AC:
332
AN:
33480
American (AMR)
AF:
AC:
10
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
0
AN:
39700
South Asian (SAS)
AF:
AC:
0
AN:
86256
European-Finnish (FIN)
AF:
AC:
0
AN:
52930
Middle Eastern (MID)
AF:
AC:
1
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1112006
Other (OTH)
AF:
AC:
38
AN:
60388
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.489
Heterozygous variant carriers
0
26
51
77
102
128
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.00293 AC: 446AN: 152344Hom.: 5 Cov.: 32 AF XY: 0.00286 AC XY: 213AN XY: 74502 show subpopulations
GnomAD4 genome
AF:
AC:
446
AN:
152344
Hom.:
Cov.:
32
AF XY:
AC XY:
213
AN XY:
74502
show subpopulations
African (AFR)
AF:
AC:
432
AN:
41584
American (AMR)
AF:
AC:
11
AN:
15306
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5178
South Asian (SAS)
AF:
AC:
1
AN:
4826
European-Finnish (FIN)
AF:
AC:
0
AN:
10630
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68026
Other (OTH)
AF:
AC:
2
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.487
Heterozygous variant carriers
0
24
47
71
94
118
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Oct 10, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational 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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