rs988920

Variant names:

• chr18-3993987-T-C
• rs988920
• NM_004746.4:c.-73+11129A>G

Your query was ambiguous. Multiple possible variants found:

• chr18-3993987-T-C
• chr18-3993987-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004746.4(DLGAP1):​c.-73+11129A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,020 control chromosomes in the GnomAD database, including 5,870 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 0.27 (5870 hom., cov: 32)
• Consequence: DLGAP1 NM_004746.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540
• Publications: 1 publications found

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]

DLGAP1-AS4 (HGNC:44333): (DLGAP1 antisense RNA 4)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004746.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLGAP1	NM_004746.4	MANE Select	c.-73+11129A>G		intron	N/A	NP_004737.2
	DLGAP1	NM_001398525.1		c.-73+11129A>G		intron	N/A	NP_001385454.1
	DLGAP1	NM_001398526.1		c.-73+11129A>G		intron	N/A	NP_001385455.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLGAP1	ENST00000315677.8	TSL:5 MANE Select	c.-73+11129A>G		intron	N/A	ENSP00000316377.3
	DLGAP1	ENST00000581550.5	TSL:1	n.324-7771A>G		intron	N/A
	DLGAP1	ENST00000581527.5	TSL:2	c.-73+11129A>G		intron	N/A	ENSP00000463864.1

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41746 AN: 151902 Hom.: 5864 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.275 AC: 41770 AN: 152020 Hom.: 5870 Cov.: 32 AF XY: 0.274 AC XY: 20405 AN XY: 74336

African (AFR) AF: 0.259 AC: 10734 AN: 41480

American (AMR) AF: 0.349 AC: 5338 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1184 AN: 3468

East Asian (EAS) AF: 0.254 AC: 1313 AN: 5166

South Asian (SAS) AF: 0.322 AC: 1541 AN: 4786

European-Finnish (FIN) AF: 0.192 AC: 2029 AN: 10588

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18597 AN: 67940

Other (OTH) AF: 0.291 AC: 615 AN: 2114

Alfa AF: 0.274 Hom.: 3560

Bravo AF: 0.282

Asia WGS AF: 0.264 AC: 919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.4
DANN	Benign	0.79
PhyloP100		0.054
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: rs988920; hg19: chr18-3993987;