rs9284410

Positions:

• chr18-4192281-G-A

Variant summary

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

The NM_004746.4(DLGAP1):​c.-266-40994C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 151,960 control chromosomes in the GnomAD database, including 7,842 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 0.32 (7842 hom., cov: 32)
• Consequence: DLGAP1 NM_004746.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.774

Genes affected

DLGAP1 (HGNC:2905): (DLG associated protein 1) Predicted to enable molecular adaptor activity. Predicted to be a structural constituent of postsynaptic density. Predicted to be involved in several processes, including aggresome assembly; regulation of postsynaptic neurotransmitter receptor activity; and regulation of proteasomal protein catabolic process. Predicted to be located in plasma membrane. Predicted to be part of postsynaptic density. Predicted to be active in glutamatergic synapse and postsynaptic density, intracellular component. [provided by Alliance of Genome Resources, Apr 2022]

LOC124904239 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLGAP1	NM_004746.4	c.-266-40994C>T		intron_variant		ENST00000315677.8
LOC124904239	XR_007066271.1	n.10582G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLGAP1	ENST00000315677.8	c.-266-40994C>T		intron_variant		5	NM_004746.4	P1
DLGAP1	ENST00000581550.5	n.130-40994C>T		intron_variant, non_coding_transcript_variant		1
DLGAP1	ENST00000581527.5	c.-266-40994C>T		intron_variant		2
DLGAP1	ENST00000577430.1	n.152-40994C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47975 AN: 151842 Hom.: 7818 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.316 AC: 48056 AN: 151960 Hom.: 7842 Cov.: 32 AF XY: 0.316 AC XY: 23458 AN XY: 74276

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.305

Alfa AF: 0.282 Hom.: 8378

Bravo AF: 0.324

Asia WGS AF: 0.313 AC: 1088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.20
DANN	Benign	0.35

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: rs9284410; hg19: chr18-4192281;