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GeneBe

1-34868711-G-A

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7

The NM_001080418.3(DLGAP3):c.2379C>T(p.Arg793=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00067 in 1,610,906 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0033 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00039 ( 4 hom. )

Consequence

DLGAP3
NM_001080418.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.102
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-34868711-G-A is Benign according to our data. Variant chr1-34868711-G-A is described in ClinVar as [Benign]. Clinvar id is 716659.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.102 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DLGAP3NM_001080418.3 linkuse as main transcriptc.2379C>T p.Arg793= synonymous_variant 9/12 ENST00000373347.6
DLGAP3XM_011541879.3 linkuse as main transcriptc.2379C>T p.Arg793= synonymous_variant 10/13
DLGAP3XM_047426631.1 linkuse as main transcriptc.2379C>T p.Arg793= synonymous_variant 9/12
DLGAP3XM_011541880.3 linkuse as main transcriptc.888C>T p.Arg296= synonymous_variant 5/8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DLGAP3ENST00000373347.6 linkuse as main transcriptc.2379C>T p.Arg793= synonymous_variant 9/125 NM_001080418.3 P1
DLGAP3ENST00000235180.4 linkuse as main transcriptc.2379C>T p.Arg793= synonymous_variant 7/102 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00334
AC:
508
AN:
152220
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0115
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00118
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000735
Gnomad OTH
AF:
0.00335
GnomAD3 exomes
AF:
0.000861
AC:
213
AN:
247498
Hom.:
1
AF XY:
0.000617
AC XY:
83
AN XY:
134532
show subpopulations
Gnomad AFR exome
AF:
0.0113
Gnomad AMR exome
AF:
0.000405
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000131
Gnomad FIN exome
AF:
0.0000518
Gnomad NFE exome
AF:
0.0000711
Gnomad OTH exome
AF:
0.000492
GnomAD4 exome
AF:
0.000393
AC:
573
AN:
1458570
Hom.:
4
Cov.:
32
AF XY:
0.000322
AC XY:
234
AN XY:
725830
show subpopulations
Gnomad4 AFR exome
AF:
0.0126
Gnomad4 AMR exome
AF:
0.000581
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.000162
Gnomad4 FIN exome
AF:
0.0000199
Gnomad4 NFE exome
AF:
0.0000522
Gnomad4 OTH exome
AF:
0.000828
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00332
AC:
506
AN:
152336
Hom.:
1
Cov.:
32
AF XY:
0.00336
AC XY:
250
AN XY:
74504
show subpopulations
Gnomad4 AFR
AF:
0.0114
Gnomad4 AMR
AF:
0.00118
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000735
Gnomad4 OTH
AF:
0.00331
Alfa
AF:
0.00195
Hom.:
0
Bravo
AF:
0.00382
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.0000545
EpiControl
AF:
0.000119

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJan 19, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.40
Cadd
Benign
15
Dann
Benign
0.81

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs77048244; hg19: chr1-35334312; API