rs11264155

Variant names:

• chr1-34891077-C-G
• rs11264155
• NM_001080418.3:c.1387-4792G>C

Variant summary

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

The NM_001080418.3(DLGAP3):​c.1387-4792G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 151,930 control chromosomes in the GnomAD database, including 16,678 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 0.46 (16678 hom., cov: 33)
• Consequence: DLGAP3 NM_001080418.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLGAP3	NM_001080418.3	c.1387-4792G>C		intron_variant	Intron 5 of 11	ENST00000373347.6	NP_001073887.1
DLGAP3	XM_011541880.3	c.-1965G>C		5_prime_UTR_variant	Exon 1 of 8		XP_011540182.1
DLGAP3	XM_011541879.3	c.1387-4792G>C		intron_variant	Intron 6 of 12		XP_011540181.1
DLGAP3	XM_047426631.1	c.1387-4792G>C		intron_variant	Intron 5 of 11		XP_047282587.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLGAP3	ENST00000373347.6	c.1387-4792G>C		intron_variant	Intron 5 of 11	5	NM_001080418.3	ENSP00000362444.1
DLGAP3	ENST00000235180.4	c.1387-4792G>C		intron_variant	Intron 3 of 9	2		ENSP00000235180.4

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69794 AN: 151814 Hom.: 16673 Cov.: 33

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.0603

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.460 AC: 69827 AN: 151930 Hom.: 16678 Cov.: 33 AF XY: 0.449 AC XY: 33322 AN XY: 74256

African (AFR) AF: 0.529 AC: 21911 AN: 41442

American (AMR) AF: 0.379 AC: 5794 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1558 AN: 3466

East Asian (EAS) AF: 0.0599 AC: 310 AN: 5178

South Asian (SAS) AF: 0.344 AC: 1660 AN: 4826

European-Finnish (FIN) AF: 0.417 AC: 4389 AN: 10532

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32631 AN: 67908

Other (OTH) AF: 0.440 AC: 929 AN: 2110

Alfa AF: 0.480 Hom.: 2197

Bravo AF: 0.461

Asia WGS AF: 0.219 AC: 763 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	0.59
DANN	Benign	0.48
PhyloP100		-0.70
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: rs11264155; hg19: chr1-35356678;