chr1-34903159-G-A

Variant names:

• chr1-34903159-G-A
• rs6686484
• NM_001080418.3:c.1107+1118C>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+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
• 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 (EAS) allele frequency at 95% confidence interval = 0.972 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+1118C>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+1118C>T		intron	N/A	ENSP00000362444.1
	DLGAP3	ENST00000235180.4	TSL:2	c.1107+1118C>T		intron	N/A	ENSP00000235180.4

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

African (AFR) AF: 0.447 AC: 18488 AN: 41406

American (AMR) AF: 0.709 AC: 10834 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2407 AN: 3468

East Asian (EAS) AF: 0.995 AC: 5139 AN: 5164

South Asian (SAS) AF: 0.791 AC: 3814 AN: 4822

European-Finnish (FIN) AF: 0.741 AC: 7853 AN: 10592

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.634 AC: 43055 AN: 67960

Other (OTH) AF: 0.607 AC: 1283 AN: 2114

Alfa AF: 0.624 Hom.: 39308

Bravo AF: 0.605

Asia WGS AF: 0.850 AC: 2956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.37
DANN	Benign	0.29
PhyloP100		-1.5
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: rs6686484; hg19: chr1-35368760;