rs763869

Variant names:

• chr8-1427444-G-A
• rs763869
• NM_001346810.2:c.107-73922G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-1427444-G-A
• chr8-1427444-G-C

Variant summary

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

The NM_001346810.2(DLGAP2):​c.107-73922G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 152,048 control chromosomes in the GnomAD database, including 21,016 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 0.52 (21016 hom., cov: 33)
• Consequence: DLGAP2 NM_001346810.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698
• Publications: 16 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 Gene-Disease associations (from GenCC):

• complex neurodevelopmental disorder

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

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 (SAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLGAP2	NM_001346810.2	c.107-73922G>A		intron_variant	Intron 3 of 14	ENST00000637795.2	NP_001333739.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLGAP2	ENST00000637795.2	c.107-73922G>A		intron_variant	Intron 3 of 14	5	NM_001346810.2	ENSP00000489774.1
DLGAP2	ENST00000421627.7	c.104-73922G>A		intron_variant	Intron 3 of 14	5		ENSP00000400258.3

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79256 AN: 151930 Hom.: 20980 Cov.: 33

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.522 AC: 79343 AN: 152048 Hom.: 21016 Cov.: 33 AF XY: 0.528 AC XY: 39208 AN XY: 74300

African (AFR) AF: 0.488 AC: 20242 AN: 41472

American (AMR) AF: 0.586 AC: 8949 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1933 AN: 3466

East Asian (EAS) AF: 0.648 AC: 3356 AN: 5176

South Asian (SAS) AF: 0.725 AC: 3493 AN: 4820

European-Finnish (FIN) AF: 0.547 AC: 5784 AN: 10568

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33817 AN: 67960

Other (OTH) AF: 0.524 AC: 1106 AN: 2112

Alfa AF: 0.509 Hom.: 31493

Bravo AF: 0.521

Asia WGS AF: 0.648 AC: 2250 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	1.5
DANN	Benign	0.59
PhyloP100		-0.70

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs763869; hg19: chr8-1375610;