rs4418368

Positions:

• chr8-1650212-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001346810.2(DLGAP2):​c.1810+17166G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 152,074 control chromosomes in the GnomAD database, including 8,807 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 0.34 (8807 hom., cov: 33)
• Consequence: DLGAP2 NM_001346810.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

Genes affected

DLGAP2 (HGNC:2906): (DLG associated protein 2) The product of this gene is a membrane-associated protein that may play a role in synapse organization and signalling in neuronal cells. This gene is biallelically expressed in the brain, however, only the paternal allele is expressed in the testis (PMID:18055845). Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jun 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DLGAP2	NM_001346810.2	c.1810+17166G>A		intron_variant		ENST00000637795.2	NP_001333739.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLGAP2	ENST00000637795.2	c.1810+17166G>A		intron_variant		5	NM_001346810.2	ENSP00000489774.1
DLGAP2	ENST00000520901.5	c.1618+17166G>A		intron_variant		1		ENSP00000430563.3
DLGAP2	ENST00000421627.7	c.1807+17166G>A		intron_variant		5		ENSP00000400258.3
DLGAP2	ENST00000612087.1	c.1570+17166G>A		intron_variant		5		ENSP00000484215.1

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51703 AN: 151954 Hom.: 8796 Cov.: 33

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.340 AC: 51751 AN: 152074 Hom.: 8807 Cov.: 33 AF XY: 0.343 AC XY: 25518 AN XY: 74342

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.340

Alfa AF: 0.346 Hom.: 1506

Bravo AF: 0.334

Asia WGS AF: 0.291 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.58

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

Publications

LitVar

Other links and lift over

dbSNP: rs4418368; hg19: chr8-1598378;