Menu
GeneBe

1-34904466-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001080418.3(DLGAP3):c.918C>T(p.Gly306=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00284 in 1,614,114 control chromosomes in the GnomAD database, including 193 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0045 ( 26 hom., cov: 32)
Exomes 𝑓: 0.0027 ( 167 hom. )

Consequence

DLGAP3
NM_001080418.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.960
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 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=-0.52).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-34904466-G-A is Benign according to our data. Variant chr1-34904466-G-A is described in ClinVar as [Benign]. Clinvar id is 778796.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=-0.96 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0642 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DLGAP3NM_001080418.3 linkuse as main transcriptc.918C>T p.Gly306= synonymous_variant 3/12 ENST00000373347.6
DLGAP3XM_011541879.3 linkuse as main transcriptc.918C>T p.Gly306= synonymous_variant 4/13
DLGAP3XM_047426631.1 linkuse as main transcriptc.918C>T p.Gly306= synonymous_variant 3/12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DLGAP3ENST00000373347.6 linkuse as main transcriptc.918C>T p.Gly306= synonymous_variant 3/125 NM_001080418.3 P1
DLGAP3ENST00000235180.4 linkuse as main transcriptc.918C>T p.Gly306= synonymous_variant 1/102 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00451
AC:
686
AN:
152180
Hom.:
25
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00125
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0352
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00502
Gnomad SAS
AF:
0.00124
Gnomad FIN
AF:
0.000942
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000529
Gnomad OTH
AF:
0.00861
GnomAD3 exomes
AF:
0.0106
AC:
2661
AN:
251106
Hom.:
144
AF XY:
0.00777
AC XY:
1055
AN XY:
135796
show subpopulations
Gnomad AFR exome
AF:
0.00130
Gnomad AMR exome
AF:
0.0692
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00539
Gnomad SAS exome
AF:
0.000523
Gnomad FIN exome
AF:
0.000788
Gnomad NFE exome
AF:
0.000493
Gnomad OTH exome
AF:
0.00945
GnomAD4 exome
AF:
0.00266
AC:
3889
AN:
1461816
Hom.:
167
Cov.:
33
AF XY:
0.00229
AC XY:
1668
AN XY:
727218
show subpopulations
Gnomad4 AFR exome
AF:
0.00102
Gnomad4 AMR exome
AF:
0.0662
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00768
Gnomad4 SAS exome
AF:
0.000510
Gnomad4 FIN exome
AF:
0.000881
Gnomad4 NFE exome
AF:
0.000298
Gnomad4 OTH exome
AF:
0.00280
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00454
AC:
692
AN:
152298
Hom.:
26
Cov.:
32
AF XY:
0.00471
AC XY:
351
AN XY:
74476
show subpopulations
Gnomad4 AFR
AF:
0.00125
Gnomad4 AMR
AF:
0.0355
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00503
Gnomad4 SAS
AF:
0.00124
Gnomad4 FIN
AF:
0.000942
Gnomad4 NFE
AF:
0.000529
Gnomad4 OTH
AF:
0.00852
Alfa
AF:
0.000977
Hom.:
1
Bravo
AF:
0.00708
Asia WGS
AF:
0.00808
AC:
28
AN:
3478
EpiCase
AF:
0.0000545
EpiControl
AF:
0.000652

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 testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.52
Cadd
Benign
2.5
Dann
Benign
0.70

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs141540099; hg19: chr1-35370067; COSMIC: COSV104580661; COSMIC: COSV104580661; API