dbSNP rs12455524: DLGAP1-AS1:n.1156G>A (chr18-3597527-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000317114.4(DLGAP1-AS1):n.1156G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0901 in 310,440 control chromosomes in the GnomAD database, including 1,513 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 0.082 ( 648 hom., cov: 32)

Exomes 𝑓: 0.098 ( 865 hom. )

Consequence

DLGAP1-AS1
ENST00000317114.4 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.241

Publications

10 publications found

Variant links:

Genes affected

DLGAP1-AS1 (HGNC:31676): (DLGAP1 antisense RNA 1)

DLGAP1-AS1 links:

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 links:

DLGAP1-AS2 (HGNC:28146): (DLGAP1 antisense RNA 2)

DLGAP1-AS2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLGAP1	NM_004746.4 link	c.1592-15279C>T		intron_variant	Intron 7 of 12	ENST00000315677.8	NP_004737.2	O14490-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLGAP1	ENST00000315677.8 link	c.1592-15279C>T		intron_variant	Intron 7 of 12	5	NM_004746.4	ENSP00000316377.3		O14490-1

Frequencies

GnomAD3 genomes

AF:

0.0818

AC:

12431

AN:

152040

Hom.:

649

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0244

Gnomad AMI

AF:

0.0571

Gnomad AMR

AF:

0.110

Gnomad ASJ

AF:

0.123

Gnomad EAS

AF:

0.155

Gnomad SAS

AF:

0.106

Gnomad FIN

AF:

0.0803

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.100

Gnomad OTH

AF:

0.108

GnomAD4 exome

AF:

0.0980

AC:

15519

AN:

158282

Hom.:

865

Cov.:

AF XY:

0.0997

AC XY:

8752

AN XY:

87794

show subpopulations

African (AFR)

AF:

0.0263

AC:

AN:

2664

American (AMR)

AF:

0.112

AC:

490

AN:

4366

Ashkenazi Jewish (ASJ)

AF:

0.124

AC:

438

AN:

3542

East Asian (EAS)

AF:

0.145

AC:

604

AN:

4170

South Asian (SAS)

AF:

0.111

AC:

3687

AN:

33178

European-Finnish (FIN)

AF:

0.0726

AC:

595

AN:

8190

Middle Eastern (MID)

AF:

0.126

AC:

AN:

556

European-Non Finnish (NFE)

AF:

0.0942

AC:

8861

AN:

94078

Other (OTH)

AF:

0.0934

AC:

704

AN:

7538

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

646

1293

1939

2586

3232

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

128

192

256

320

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0818

AC:

12441

AN:

152158

Hom.:

648

Cov.:

AF XY:

0.0815

AC XY:

6063

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.0244

AC:

1012

AN:

41532

American (AMR)

AF:

0.111

AC:

1691

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.123

AC:

426

AN:

3468

East Asian (EAS)

AF:

0.155

AC:

802

AN:

5178

South Asian (SAS)

AF:

0.107

AC:

515

AN:

4816

European-Finnish (FIN)

AF:

0.0803

AC:

850

AN:

10588

Middle Eastern (MID)

AF:

0.150

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.100

AC:

6824

AN:

67984

Other (OTH)

AF:

0.107

AC:

225

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

601

1202

1802

2403

3004

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

150

300

450

600

750

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0978

Hom.:

1346

Bravo

AF:

0.0840

Asia WGS

AF:

0.104

AC:

364

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.98

(source)

DANN

Benign

0.65

PhyloP100

-0.24

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over