8-1583058-T-C

Variant names:

• chr8-1583058-T-C
• rs6558484
• NM_001346810.2:c.1442+17164T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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-AS1 (HGNC:50467): (DLGAP2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLGAP2	NM_001346810.2	MANE Select	c.1442+17164T>C		intron	N/A	NP_001333739.1	A0A1B0GTN4
	DLGAP2-AS1	NR_103863.1		n.358-17320A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLGAP2	ENST00000637795.2	TSL:5 MANE Select	c.1442+17164T>C		intron	N/A	ENSP00000489774.1	A0A1B0GTN4
	DLGAP2	ENST00000520901.5	TSL:1	c.1250+17164T>C		intron	N/A	ENSP00000430563.3	H0YBY6
	DLGAP2	ENST00000421627.7	TSL:5	c.1439+17164T>C		intron	N/A	ENSP00000400258.3	Q9P1A6-1

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

African (AFR) AF: 0.748 AC: 31006 AN: 41470

American (AMR) AF: 0.461 AC: 7038 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1783 AN: 3470

East Asian (EAS) AF: 0.561 AC: 2902 AN: 5174

South Asian (SAS) AF: 0.476 AC: 2287 AN: 4808

European-Finnish (FIN) AF: 0.514 AC: 5425 AN: 10554

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35116 AN: 67968

Other (OTH) AF: 0.553 AC: 1165 AN: 2108

Alfa AF: 0.504 Hom.: 9346

Bravo AF: 0.576

Asia WGS AF: 0.540 AC: 1878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.015
DANN	Benign	0.21
PhyloP100		-4.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6558484; hg19: chr8-1531224;