rs6686484

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001080418.3(DLGAP3):​c.1107+1118C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 152,008 control chromosomes in the GnomAD database, including 30,050 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.62 ( 30050 hom., cov: 32)

Consequence

DLGAP3
NM_001080418.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.46
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 Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DLGAP3NM_001080418.3 linkuse as main transcriptc.1107+1118C>T intron_variant ENST00000373347.6 NP_001073887.1
DLGAP3XM_011541879.3 linkuse as main transcriptc.1107+1118C>T intron_variant XP_011540181.1
DLGAP3XM_047426631.1 linkuse as main transcriptc.1107+1118C>T intron_variant XP_047282587.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DLGAP3ENST00000373347.6 linkuse as main transcriptc.1107+1118C>T intron_variant 5 NM_001080418.3 ENSP00000362444 P1
DLGAP3ENST00000235180.4 linkuse as main transcriptc.1107+1118C>T intron_variant 2 ENSP00000235180 P1

Frequencies

GnomAD3 genomes
AF:
0.616
AC:
93537
AN:
151890
Hom.:
30012
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.446
Gnomad AMI
AF:
0.663
Gnomad AMR
AF:
0.709
Gnomad ASJ
AF:
0.694
Gnomad EAS
AF:
0.995
Gnomad SAS
AF:
0.791
Gnomad FIN
AF:
0.741
Gnomad MID
AF:
0.541
Gnomad NFE
AF:
0.634
Gnomad OTH
AF:
0.603
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.616
AC:
93635
AN:
152008
Hom.:
30050
Cov.:
32
AF XY:
0.628
AC XY:
46647
AN XY:
74322
show subpopulations
Gnomad4 AFR
AF:
0.447
Gnomad4 AMR
AF:
0.709
Gnomad4 ASJ
AF:
0.694
Gnomad4 EAS
AF:
0.995
Gnomad4 SAS
AF:
0.791
Gnomad4 FIN
AF:
0.741
Gnomad4 NFE
AF:
0.634
Gnomad4 OTH
AF:
0.607
Alfa
AF:
0.630
Hom.:
30532
Bravo
AF:
0.605
Asia WGS
AF:
0.850
AC:
2956
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.37
DANN
Benign
0.29

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: rs6686484; hg19: chr1-35368760; API