chr18-3514317-C-T

Variant names:

• chr18-3514317-C-T
• rs17802670
• NM_004746.4:c.2480-5656G>A

Variant summary

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

The NM_001398525.1(DLGAP1):​c.2510-5656G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0576 in 152,166 control chromosomes in the GnomAD database, including 339 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 0.058 (339 hom., cov: 32)
• Consequence: DLGAP1 NM_001398525.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 1 publications found

Genes affected

DLGAP1 (HGNC:2905): (DLG associated protein 1) Predicted to enable molecular adaptor activity. Predicted to be a structural constituent of postsynaptic density. Predicted to be involved in several processes, including aggresome assembly; regulation of postsynaptic neurotransmitter receptor activity; and regulation of proteasomal protein catabolic process. Predicted to be located in plasma membrane. Predicted to be part of postsynaptic density. Predicted to be active in glutamatergic synapse and postsynaptic density, intracellular component. [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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0763 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001398525.1. 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
	DLGAP1	NM_004746.4	MANE Select	c.2480-5656G>A		intron	N/A	NP_004737.2
	DLGAP1	NM_001398525.1		c.2510-5656G>A		intron	N/A	NP_001385454.1
	DLGAP1	NM_001398526.1		c.2510-5656G>A		intron	N/A	NP_001385455.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLGAP1	ENST00000315677.8	TSL:5 MANE Select	c.2480-5656G>A		intron	N/A	ENSP00000316377.3
	DLGAP1	ENST00000400147.6	TSL:1	c.1574-5656G>A		intron	N/A	ENSP00000383011.2
	DLGAP1	ENST00000400145.6	TSL:1	c.1574-5656G>A		intron	N/A	ENSP00000383010.2

Frequencies

GnomAD3 genomes AF: 0.0576 AC: 8756 AN: 152048 Hom.: 339 Cov.: 32

Gnomad AFR AF: 0.0261

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.0796

Gnomad ASJ AF: 0.0326

Gnomad EAS AF: 0.00309

Gnomad SAS AF: 0.0625

Gnomad FIN AF: 0.0747

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0726

Gnomad OTH AF: 0.0721

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

GnomAD4 genome AF: 0.0576 AC: 8761 AN: 152166 Hom.: 339 Cov.: 32 AF XY: 0.0583 AC XY: 4339 AN XY: 74394

African (AFR) AF: 0.0261 AC: 1083 AN: 41520

American (AMR) AF: 0.0800 AC: 1222 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0326 AC: 113 AN: 3470

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5172

South Asian (SAS) AF: 0.0615 AC: 297 AN: 4828

European-Finnish (FIN) AF: 0.0747 AC: 790 AN: 10578

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0726 AC: 4940 AN: 67998

Other (OTH) AF: 0.0714 AC: 151 AN: 2116

Alfa AF: 0.0686 Hom.: 778

Bravo AF: 0.0551

Asia WGS AF: 0.0310 AC: 111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.74
DANN	Benign	0.38
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: rs17802670; hg19: chr18-3514315;