rs10503166

chr8-1541752-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.173-6874A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0862 in 152,268 control chromosomes in the GnomAD database, including 780 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 0.086 (780 hom., cov: 33)
• Consequence: DLGAP2 NM_001346810.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLGAP2	NM_001346810.2	c.173-6874A>G		intron_variant		ENST00000637795.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLGAP2	ENST00000637795.2	c.173-6874A>G		intron_variant		5	NM_001346810.2
DLGAP2	ENST00000421627.7	c.170-6874A>G		intron_variant		5
DLGAP2	ENST00000612087.1	c.-68-6874A>G		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.0863 AC: 13128 AN: 152150 Hom.: 780 Cov.: 33

Gnomad AFR AF: 0.0232

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0739

Gnomad ASJ AF: 0.0772

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.0862 AC: 13122 AN: 152268 Hom.: 780 Cov.: 33 AF XY: 0.0850 AC XY: 6329 AN XY: 74454

Gnomad4 AFR AF: 0.0231

Gnomad4 AMR AF: 0.0738

Gnomad4 ASJ AF: 0.0772

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0224

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.0799

Alfa AF: 0.113 Hom.: 633

Bravo AF: 0.0808

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.64
Dann	Benign	0.56

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10503166; hg19: chr8-1489918;