dbSNP rs1650146: DLG5:c.-27+12220T>C (chr10-77928450-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NR_024585.1(DLG5-AS1):n.1639A>G 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 0.719 in 152,202 control chromosomes in the GnomAD database, including 40,737 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 0.72 ( 40721 hom., cov: 32)

Exomes 𝑓: 0.66 ( 16 hom. )

Consequence

DLG5-AS1
NR_024585.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.856

Publications

4 publications found

Variant links:

Genes affected

DLG5 (HGNC:2904): (discs large MAGUK scaffold protein 5) This gene encodes a member of the family of discs large (DLG) homologs, a subset of the membrane-associated guanylate kinase (MAGUK) superfamily. The MAGUK proteins are composed of a catalytically inactive guanylate kinase domain, in addition to PDZ and SH3 domains, and are thought to function as scaffolding molecules at sites of cell-cell contact. The protein encoded by this gene localizes to the plasma membrane and cytoplasm, and interacts with components of adherens junctions and the cytoskeleton. It is proposed to function in the transmission of extracellular signals to the cytoskeleton and in the maintenance of epithelial cell structure. Alternative splice variants have been described but their biological nature has not been determined. [provided by RefSeq, Jul 2008]

DLG5 links:

DLG5-AS1 (HGNC:45109): (DLG5 antisense RNA 1)

DLG5-AS1 links:

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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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_024585.1. 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
	DLG5-AS1	NR_024585.1		n.1639A>G		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
DLG5-AS1	ENST00000632919.1	TSL:6	n.820A>G	non_coding_transcript_exon	Exon 1 of 1
DLG5-AS1	ENST00000449852.2	TSL:2	n.450+828A>G	intron	N/A
DLG5-AS1	ENST00000842780.1		n.628-1139A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.718

AC:

109201

AN:

152020

Hom.:

40659

Cov.:

show subpopulations

Gnomad AFR

AF:

0.924

Gnomad AMI

AF:

0.770

Gnomad AMR

AF:

0.734

Gnomad ASJ

AF:

0.620

Gnomad EAS

AF:

0.772

Gnomad SAS

AF:

0.651

Gnomad FIN

AF:

0.582

Gnomad MID

AF:

0.617

Gnomad NFE

AF:

0.617

Gnomad OTH

AF:

0.694

GnomAD4 exome

AF:

0.656

AC:

AN:

Hom.:

Cov.:

AF XY:

0.646

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

0.750

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.640

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.719

AC:

109324

AN:

152138

Hom.:

40721

Cov.:

AF XY:

0.715

AC XY:

53175

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.924

AC:

38394

AN:

41558

American (AMR)

AF:

0.734

AC:

11219

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.620

AC:

2152

AN:

3470

East Asian (EAS)

AF:

0.772

AC:

3979

AN:

5152

South Asian (SAS)

AF:

0.650

AC:

3130

AN:

4814

European-Finnish (FIN)

AF:

0.582

AC:

6155

AN:

10574

Middle Eastern (MID)

AF:

0.616

AC:

181

AN:

294

European-Non Finnish (NFE)

AF:

0.617

AC:

41947

AN:

67980

Other (OTH)

AF:

0.695

AC:

1465

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1489

2978

4468

5957

7446

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

818

1636

2454

3272

4090

<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:

0.675

Hom.:

8597

Bravo

AF:

0.740

Asia WGS

AF:

0.764

AC:

2658

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

7.2

(source)

DANN

Benign

0.46

PhyloP100

0.86

Splicing

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over