8-1652979-G-T

Variant names:

• chr8-1652979-G-T
• rs17064176
• NM_001346810.2:c.1811-15350G>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.1811-15350G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 151,948 control chromosomes in the GnomAD database, including 9,294 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 0.35 (9294 hom., cov: 32)
• Consequence: DLGAP2 NM_001346810.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.852
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLGAP2	NM_001346810.2	c.1811-15350G>T		intron_variant	Intron 8 of 14	ENST00000637795.2	NP_001333739.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLGAP2	ENST00000637795.2	c.1811-15350G>T		intron_variant	Intron 8 of 14	5	NM_001346810.2	ENSP00000489774.1
DLGAP2	ENST00000520901.5	c.1619-15350G>T		intron_variant	Intron 4 of 9	1		ENSP00000430563.3
DLGAP2	ENST00000421627.7	c.1808-15350G>T		intron_variant	Intron 8 of 14	5		ENSP00000400258.3
DLGAP2	ENST00000612087.1	c.1571-15350G>T		intron_variant	Intron 5 of 10	5		ENSP00000484215.1

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53042 AN: 151828 Hom.: 9279 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.349 AC: 53098 AN: 151948 Hom.: 9294 Cov.: 32 AF XY: 0.353 AC XY: 26204 AN XY: 74278

African (AFR) AF: 0.345 AC: 14293 AN: 41422

American (AMR) AF: 0.364 AC: 5558 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1052 AN: 3470

East Asian (EAS) AF: 0.390 AC: 2004 AN: 5142

South Asian (SAS) AF: 0.279 AC: 1342 AN: 4816

European-Finnish (FIN) AF: 0.401 AC: 4236 AN: 10552

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23530 AN: 67956

Other (OTH) AF: 0.351 AC: 741 AN: 2110

Alfa AF: 0.250 Hom.: 716

Bravo AF: 0.349

Asia WGS AF: 0.317 AC: 1101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.067
DANN	Benign	0.53
PhyloP100		-0.85
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: rs17064176; hg19: chr8-1601145;