rs12541553

chr8-1359860-C-Achr8-1359860-C-Gchr8-1359860-C-T

Variant summary

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

The NM_001346810.2(DLGAP2):c.106+100977C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 152,130 control chromosomes in the GnomAD database, including 25,763 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 0.58 (25763 hom., cov: 34)
• Consequence: DLGAP2 NM_001346810.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLGAP2	NM_001346810.2	c.106+100977C>A		intron_variant		ENST00000637795.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLGAP2	ENST00000637795.2	c.106+100977C>A		intron_variant		5	NM_001346810.2
DLGAP2	ENST00000421627.7	c.103+100977C>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87584 AN: 152012 Hom.: 25732 Cov.: 34

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.474

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.576 AC: 87678 AN: 152130 Hom.: 25763 Cov.: 34 AF XY: 0.583 AC XY: 43348 AN XY: 74382

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.547

Gnomad4 EAS AF: 0.928

Gnomad4 SAS AF: 0.617

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.551

Alfa AF: 0.533 Hom.: 28405

Bravo AF: 0.571

Asia WGS AF: 0.769 AC: 2677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.2
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12541553; hg19: chr8-1308026;