Genetic Variant DLGAP1:p.Pro517Pro (chr18-3729175-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BA1

The NM_004746.4(DLGAP1):c.1551G>A(p.Pro517Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 1,612,722 control chromosomes in the GnomAD database, including 18,210 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.18 ( 3235 hom., cov: 32)

Exomes 𝑓: 0.13 ( 14975 hom. )

Consequence

DLGAP1
NM_004746.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.480

Variant links:

Genes affected

DLGAP1 (HGNC:2905): (DLG associated protein 1) Predicted to enable molecular adaptor activity. Predicted to be a structural constituent of postsynaptic density. Predicted to be involved in several processes, including aggresome assembly; regulation of postsynaptic neurotransmitter receptor activity; and regulation of proteasomal protein catabolic process. Predicted to be located in plasma membrane. Predicted to be part of postsynaptic density. Predicted to be active in glutamatergic synapse and postsynaptic density, intracellular component. [provided by Alliance of Genome Resources, Apr 2022]

DLGAP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.41).

BP6

Variant 18-3729175-C-T is Benign according to our data. Variant chr18-3729175-C-T is described in ClinVar as [Benign]. Clinvar id is 3060604.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.48 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLGAP1	NM_004746.4 link	c.1551G>A	p.Pro517Pro	synonymous_variant	Exon 7 of 13	ENST00000315677.8	NP_004737.2	O14490-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLGAP1	ENST00000315677.8 link	c.1551G>A	p.Pro517Pro	synonymous_variant	Exon 7 of 13	5	NM_004746.4	ENSP00000316377.3		O14490-1

Frequencies

GnomAD3 genomes

AF:

0.183

AC:

27791

AN:

151956

Hom.:

3232

Cov.:

show subpopulations

Gnomad AFR

AF:

0.303

Gnomad AMI

AF:

0.109

Gnomad AMR

AF:

0.141

Gnomad ASJ

AF:

0.163

Gnomad EAS

AF:

0.345

Gnomad SAS

AF:

0.224

Gnomad FIN

AF:

0.165

Gnomad MID

AF:

0.143

Gnomad NFE

AF:

0.110

Gnomad OTH

AF:

0.170

GnomAD3 exomes

AF:

0.163

AC:

40490

AN:

247898

Hom.:

4006

AF XY:

0.161

AC XY:

21571

AN XY:

134372

show subpopulations

Gnomad AFR exome

AF:

0.313

Gnomad AMR exome

AF:

0.133

Gnomad ASJ exome

AF:

0.170

Gnomad EAS exome

AF:

0.335

Gnomad SAS exome

AF:

0.217

Gnomad FIN exome

AF:

0.163

Gnomad NFE exome

AF:

0.109

Gnomad OTH exome

AF:

0.150

GnomAD4 exome

AF:

0.131

AC:

190888

AN:

1460646

Hom.:

14975

Cov.:

AF XY:

0.133

AC XY:

96739

AN XY:

726602

show subpopulations

Gnomad4 AFR exome

AF:

0.304

Gnomad4 AMR exome

AF:

0.137

Gnomad4 ASJ exome

AF:

0.169

Gnomad4 EAS exome

AF:

0.337

Gnomad4 SAS exome

AF:

0.219

Gnomad4 FIN exome

AF:

0.150

Gnomad4 NFE exome

AF:

0.107

Gnomad4 OTH exome

AF:

0.157

GnomAD4 genome

AF:

0.183

AC:

27812

AN:

152076

Hom.:

3235

Cov.:

AF XY:

0.185

AC XY:

13771

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.303

Gnomad4 AMR

AF:

0.141

Gnomad4 ASJ

AF:

0.163

Gnomad4 EAS

AF:

0.346

Gnomad4 SAS

AF:

0.224

Gnomad4 FIN

AF:

0.165

Gnomad4 NFE

AF:

0.110

Gnomad4 OTH

AF:

0.166

Alfa

AF:

0.129

Hom.:

1993

Bravo

AF:

0.186

Asia WGS

AF:

0.249

AC:

865

AN:

3478

EpiCase

AF:

0.119

EpiControl

AF:

0.112

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

DLGAP1-related disorder

Benign:1

Oct 22, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

6.9

DANN

Benign

0.68

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over