rs10493064

Variant names:

• chr1-34903413-T-A
• rs10493064
• NM_001080418.3:c.1107+864A>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.1107+864A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,212 control chromosomes in the GnomAD database, including 2,767 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 0.18 (2767 hom., cov: 33)
• Consequence: DLGAP3 NM_001080418.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181
• Publications: 3 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 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.1107+864A>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.1107+864A>T		intron	N/A	ENSP00000362444.1
	DLGAP3	ENST00000235180.4	TSL:2	c.1107+864A>T		intron	N/A	ENSP00000235180.4

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26773 AN: 152092 Hom.: 2767 Cov.: 33

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.176 AC: 26779 AN: 152212 Hom.: 2767 Cov.: 33 AF XY: 0.181 AC XY: 13470 AN XY: 74396

African (AFR) AF: 0.126 AC: 5247 AN: 41546

American (AMR) AF: 0.274 AC: 4184 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 484 AN: 3470

East Asian (EAS) AF: 0.441 AC: 2279 AN: 5166

South Asian (SAS) AF: 0.262 AC: 1262 AN: 4826

European-Finnish (FIN) AF: 0.213 AC: 2258 AN: 10592

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10495 AN: 68000

Other (OTH) AF: 0.167 AC: 354 AN: 2116

Alfa AF: 0.160 Hom.: 283

Bravo AF: 0.177

Asia WGS AF: 0.294 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.1
DANN	Benign	0.42
PhyloP100		0.18
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: rs10493064; hg19: chr1-35369014;