rs12541553

Variant names:

• chr8-1359860-C-A
• rs12541553
• NM_001346810.2:c.106+100977C>A

Your query was ambiguous. Multiple possible variants found:

• chr8-1359860-C-A
• chr8-1359860-C-G
• chr8-1359860-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 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.106+100977C>A		intron	N/A	NP_001333739.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLGAP2	ENST00000637795.2	TSL:5 MANE Select	c.106+100977C>A		intron	N/A	ENSP00000489774.1
	DLGAP2	ENST00000421627.7	TSL:5	c.103+100977C>A		intron	N/A	ENSP00000400258.3

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

African (AFR) AF: 0.617 AC: 25606 AN: 41510

American (AMR) AF: 0.522 AC: 7980 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1898 AN: 3470

East Asian (EAS) AF: 0.928 AC: 4785 AN: 5158

South Asian (SAS) AF: 0.617 AC: 2977 AN: 4826

European-Finnish (FIN) AF: 0.630 AC: 6662 AN: 10582

Middle Eastern (MID) AF: 0.476 AC: 137 AN: 288

European-Non Finnish (NFE) AF: 0.531 AC: 36121 AN: 67988

Other (OTH) AF: 0.551 AC: 1165 AN: 2116

Alfa AF: 0.536 Hom.: 36634

Bravo AF: 0.571

Asia WGS AF: 0.769 AC: 2677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs12541553; hg19: chr8-1308026;