8-1583881-A-G

Variant names:

• chr8-1583881-A-G
• rs7014992
• NM_001346810.2:c.1442+17987A>G

Variant summary

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

The NM_001346810.2(DLGAP2):​c.1442+17987A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 151,622 control chromosomes in the GnomAD database, including 25,662 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 0.57 (25662 hom., cov: 30)
• Consequence: DLGAP2 NM_001346810.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560
• Publications: 5 publications found

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]

DLGAP2-AS1 (HGNC:50467): (DLGAP2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLGAP2	NM_001346810.2	c.1442+17987A>G		intron_variant	Intron 6 of 14	ENST00000637795.2	NP_001333739.1
DLGAP2-AS1	NR_103863.1	n.358-18143T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLGAP2	ENST00000637795.2	c.1442+17987A>G		intron_variant	Intron 6 of 14	5	NM_001346810.2	ENSP00000489774.1

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86688 AN: 151504 Hom.: 25635 Cov.: 30

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.572 AC: 86765 AN: 151622 Hom.: 25662 Cov.: 30 AF XY: 0.567 AC XY: 41974 AN XY: 74010

African (AFR) AF: 0.739 AC: 30584 AN: 41410

American (AMR) AF: 0.461 AC: 7013 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1784 AN: 3464

East Asian (EAS) AF: 0.565 AC: 2877 AN: 5088

South Asian (SAS) AF: 0.477 AC: 2286 AN: 4794

European-Finnish (FIN) AF: 0.517 AC: 5410 AN: 10470

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35077 AN: 67860

Other (OTH) AF: 0.550 AC: 1159 AN: 2106

Alfa AF: 0.521 Hom.: 11487

Bravo AF: 0.572

Asia WGS AF: 0.541 AC: 1883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.27
PhyloP100		-0.56
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: rs7014992; hg19: chr8-1532047;