rs7525948

Variant names:

• chr1-34888303-G-A
• rs7525948
• NM_001080418.3:c.1387-2018C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001080418.3(DLGAP3):​c.1387-2018C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0525 in 152,196 control chromosomes in the GnomAD database, including 371 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 0.052 (371 hom., cov: 32)
• Consequence: DLGAP3 NM_001080418.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080418.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLGAP3	NM_001080418.3	MANE Select	c.1387-2018C>T		intron	N/A	NP_001073887.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLGAP3	ENST00000373347.6	TSL:5 MANE Select	c.1387-2018C>T		intron	N/A	ENSP00000362444.1
	DLGAP3	ENST00000235180.4	TSL:2	c.1387-2018C>T		intron	N/A	ENSP00000235180.4

Frequencies

GnomAD3 genomes AF: 0.0524 AC: 7974 AN: 152076 Hom.: 367 Cov.: 32

Gnomad AFR AF: 0.0303

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0550

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.0872

Gnomad FIN AF: 0.0325

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0377

Gnomad OTH AF: 0.0660

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0525 AC: 7990 AN: 152196 Hom.: 371 Cov.: 32 AF XY: 0.0551 AC XY: 4096 AN XY: 74400

African (AFR) AF: 0.0303 AC: 1258 AN: 41508

American (AMR) AF: 0.131 AC: 1996 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0550 AC: 191 AN: 3470

East Asian (EAS) AF: 0.204 AC: 1053 AN: 5174

South Asian (SAS) AF: 0.0869 AC: 419 AN: 4824

European-Finnish (FIN) AF: 0.0325 AC: 345 AN: 10602

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0377 AC: 2564 AN: 68012

Other (OTH) AF: 0.0653 AC: 138 AN: 2114

Alfa AF: 0.0412 Hom.: 82

Bravo AF: 0.0574

Asia WGS AF: 0.124 AC: 428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.8
DANN	Benign	0.71
PhyloP100		-0.053
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7525948; hg19: chr1-35353904;