rs6686484

Positions:

• chr1-34903159-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

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]

ACMG classification

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	UniProt
DLGAP3	NM_001080418.3	c.1107+1118C>T		intron_variant		ENST00000373347.6
DLGAP3	XM_011541879.3	c.1107+1118C>T		intron_variant
DLGAP3	XM_047426631.1	c.1107+1118C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLGAP3	ENST00000373347.6	c.1107+1118C>T		intron_variant		5	NM_001080418.3	P1
DLGAP3	ENST00000235180.4	c.1107+1118C>T		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93537 AN: 151890 Hom.: 30012 Cov.: 32

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

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

Other links and lift over

dbSNP: rs6686484; hg19: chr1-35368760;