rs17669535

chr8-1295964-C-G

Variant summary

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

The NM_001346810.2(DLGAP2):c.106+37081C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0765 in 152,270 control chromosomes in the GnomAD database, including 608 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 0.076 (608 hom., cov: 33)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: DLGAP2 NM_001346810.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.732

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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLGAP2	NM_001346810.2	c.106+37081C>G		intron_variant		ENST00000637795.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLGAP2	ENST00000637795.2	c.106+37081C>G		intron_variant		5	NM_001346810.2
DLGAP2	ENST00000421627.7	c.103+37081C>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0766 AC: 11657 AN: 152148 Hom.: 610 Cov.: 33

Gnomad AFR AF: 0.0183

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0676

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0962

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0987

Gnomad OTH AF: 0.0860

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 FIN exome AF: 0.500

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0765 AC: 11642 AN: 152266 Hom.: 608 Cov.: 33 AF XY: 0.0789 AC XY: 5874 AN XY: 74446

Gnomad4 AFR AF: 0.0182

Gnomad4 AMR AF: 0.0674

Gnomad4 ASJ AF: 0.0942

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.0962

Gnomad4 NFE AF: 0.0987

Gnomad4 OTH AF: 0.0837

Alfa AF: 0.0789 Hom.: 68

Bravo AF: 0.0699

Asia WGS AF: 0.123 AC: 431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	6.5
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17669535; hg19: chr8-1244224;