rs7009367

Variant names:

• chr8-800278-A-G
• rs7009367
• NM_001346810.2:c.18+62453A>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.18+62453A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,160 control chromosomes in the GnomAD database, including 6,040 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 0.25 (6040 hom., cov: 34)
• Consequence: DLGAP2 NM_001346810.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.419
• 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 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001346810.2. 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
	DLGAP2	NM_001346810.2	MANE Select	c.18+62453A>G		intron	N/A	NP_001333739.1
	DLGAP2	NR_073397.2		n.199-21814A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLGAP2	ENST00000637795.2	TSL:5 MANE Select	c.18+62453A>G		intron	N/A	ENSP00000489774.1
	DLGAP2	ENST00000522092.5	TSL:1	n.176-21814A>G		intron	N/A
	DLGAP2	ENST00000577187.5	TSL:2	n.85-21814A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38151 AN: 152044 Hom.: 6035 Cov.: 34

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.251 AC: 38180 AN: 152160 Hom.: 6040 Cov.: 34 AF XY: 0.243 AC XY: 18053 AN XY: 74394

African (AFR) AF: 0.445 AC: 18443 AN: 41482

American (AMR) AF: 0.170 AC: 2602 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 870 AN: 3468

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5182

South Asian (SAS) AF: 0.161 AC: 778 AN: 4822

European-Finnish (FIN) AF: 0.143 AC: 1517 AN: 10604

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13211 AN: 68002

Other (OTH) AF: 0.238 AC: 502 AN: 2112

Alfa AF: 0.219 Hom.: 11521

Bravo AF: 0.261

Asia WGS AF: 0.0900 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.2
DANN	Benign	0.41
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs7009367; hg19: chr8-750278;