Variant 1-34904466-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001080418.3(DLGAP3):c.918C>T(p.Gly306Gly) 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

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

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]

DLGAP3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

BP6

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_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.96 with no splicing effect.

BA1

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	Protein	UniProt
DLGAP3	NM_001080418.3 linkuse as main transcript	c.918C>T	p.Gly306Gly	synonymous_variant	3/12	ENST00000373347.6	NP_001073887.1	O95886
DLGAP3	XM_011541879.3 linkuse as main transcript	c.918C>T	p.Gly306Gly	synonymous_variant	4/13		XP_011540181.1	O95886
DLGAP3	XM_047426631.1 linkuse as main transcript	c.918C>T	p.Gly306Gly	synonymous_variant	3/12		XP_047282587.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLGAP3	ENST00000373347.6 linkuse as main transcript	c.918C>T	p.Gly306Gly	synonymous_variant	3/12	5	NM_001080418.3	ENSP00000362444.1		O95886
DLGAP3	ENST00000235180.4 linkuse as main transcript	c.918C>T	p.Gly306Gly	synonymous_variant	1/10	2		ENSP00000235180.4		O95886

Frequencies

GnomAD3 genomes

AF:

0.00451

AC:

686

AN:

152180

Hom.:

Cov.:

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.:

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

AF:

0.00454

AC:

692

AN:

152298

Hom.:

Cov.:

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.:

Bravo

AF:

0.00708

Asia WGS

AF:

0.00808

AC:

AN:

3478

EpiCase

AF:

0.0000545

EpiControl

AF:

0.000652

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 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.

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