chr8-1583058-T-C

Position:

• chr8-1583058-T-C

Variant summary

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

The NM_001346810.2(DLGAP2):​c.1442+17164T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 152,018 control chromosomes in the GnomAD database, including 25,990 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 0.57 (25990 hom., cov: 32)
• Consequence: DLGAP2 NM_001346810.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.96

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-AS1 (HGNC:50467): (DLGAP2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DLGAP2	NM_001346810.2	c.1442+17164T>C		intron_variant		ENST00000637795.2	NP_001333739.1
DLGAP2-AS1	NR_103863.1	n.358-17320A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLGAP2	ENST00000637795.2	c.1442+17164T>C		intron_variant		5	NM_001346810.2	ENSP00000489774
DLGAP2-AS1	ENST00000518063.5	n.358-17320A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87221 AN: 151900 Hom.: 25963 Cov.: 32

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.574 AC: 87297 AN: 152018 Hom.: 25990 Cov.: 32 AF XY: 0.568 AC XY: 42229 AN XY: 74304

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.553

Alfa AF: 0.497 Hom.: 8013

Bravo AF: 0.576

Asia WGS AF: 0.540 AC: 1878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.015
DANN	Benign	0.21

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: rs6558484; hg19: chr8-1531224;