1-34901689-G-T

Variant names:

• chr1-34901689-G-T
• rs4652867
• NM_001080418.3:c.1108-1416C>A

Variant summary

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

The NM_001080418.3(DLGAP3):​c.1108-1416C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,108 control chromosomes in the GnomAD database, including 6,180 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 0.25 (6180 hom., cov: 32)
• Consequence: DLGAP3 NM_001080418.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 8 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLGAP3	NM_001080418.3	c.1108-1416C>A		intron_variant	Intron 3 of 11	ENST00000373347.6	NP_001073887.1
DLGAP3	XM_011541879.3	c.1108-1416C>A		intron_variant	Intron 4 of 12		XP_011540181.1
DLGAP3	XM_047426631.1	c.1108-1416C>A		intron_variant	Intron 3 of 11		XP_047282587.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLGAP3	ENST00000373347.6	c.1108-1416C>A		intron_variant	Intron 3 of 11	5	NM_001080418.3	ENSP00000362444.1
DLGAP3	ENST00000235180.4	c.1108-1416C>A		intron_variant	Intron 1 of 9	2		ENSP00000235180.4

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38220 AN: 151990 Hom.: 6173 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.251 AC: 38233 AN: 152108 Hom.: 6180 Cov.: 32 AF XY: 0.265 AC XY: 19683 AN XY: 74338

African (AFR) AF: 0.110 AC: 4556 AN: 41518

American (AMR) AF: 0.307 AC: 4692 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 930 AN: 3470

East Asian (EAS) AF: 0.783 AC: 4047 AN: 5168

South Asian (SAS) AF: 0.417 AC: 2007 AN: 4810

European-Finnish (FIN) AF: 0.388 AC: 4099 AN: 10556

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.249 AC: 16942 AN: 67988

Other (OTH) AF: 0.275 AC: 580 AN: 2112

Alfa AF: 0.253 Hom.: 11455

Bravo AF: 0.241

Asia WGS AF: 0.541 AC: 1878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.22
DANN	Benign	0.71
PhyloP100		-1.1
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: rs4652867; hg19: chr1-35367290;