rs7009367

Positions:

• chr8-800278-A-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DLGAP2	NM_001346810.2	c.18+62453A>G		intron_variant		ENST00000637795.2	NP_001333739.1
DLGAP2	NR_073397.2	n.199-21814A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLGAP2	ENST00000637795.2	c.18+62453A>G		intron_variant		5	NM_001346810.2	ENSP00000489774
DLGAP2	ENST00000522092.5	n.176-21814A>G		intron_variant, non_coding_transcript_variant		1
DLGAP2	ENST00000577187.5	n.85-21814A>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.445

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.238

Alfa AF: 0.203 Hom.: 5722

Bravo AF: 0.261

Asia WGS AF: 0.0900 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7009367; hg19: chr8-750278;