rs6662980

Variant names:

• chr1-34894477-A-G
• rs6662980
• NM_001080418.3:c.1386+5192T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-34894477-A-G
• chr1-34894477-A-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.1386+5192T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,074 control chromosomes in the GnomAD database, including 7,652 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 0.31 (7652 hom., cov: 32)
• Consequence: DLGAP3 NM_001080418.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.784
• Publications: 14 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLGAP3	NM_001080418.3	c.1386+5192T>C		intron_variant	Intron 5 of 11	ENST00000373347.6	NP_001073887.1
DLGAP3	XM_011541879.3	c.1386+5192T>C		intron_variant	Intron 6 of 12		XP_011540181.1
DLGAP3	XM_047426631.1	c.1386+5192T>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.1386+5192T>C		intron_variant	Intron 5 of 11	5	NM_001080418.3	ENSP00000362444.1
DLGAP3	ENST00000235180.4	c.1386+5192T>C		intron_variant	Intron 3 of 9	2		ENSP00000235180.4

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47266 AN: 151954 Hom.: 7647 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.0523

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.295

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.311 AC: 47286 AN: 152074 Hom.: 7652 Cov.: 32 AF XY: 0.300 AC XY: 22336 AN XY: 74350

African (AFR) AF: 0.324 AC: 13410 AN: 41452

American (AMR) AF: 0.291 AC: 4448 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1116 AN: 3466

East Asian (EAS) AF: 0.0519 AC: 269 AN: 5184

South Asian (SAS) AF: 0.225 AC: 1084 AN: 4828

European-Finnish (FIN) AF: 0.224 AC: 2362 AN: 10560

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.344 AC: 23390 AN: 67982

Other (OTH) AF: 0.297 AC: 626 AN: 2110

Alfa AF: 0.328 Hom.: 27614

Bravo AF: 0.320

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.2
DANN	Benign	0.83
PhyloP100		0.78
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: rs6662980; hg19: chr1-35360078;