dbSNP rs3803539: GABARAPL3:n.1164A>G (chr15-90348750-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_028287.1(GABARAPL3):n.698T>C 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 0.219 in 569,552 control chromosomes in the GnomAD database, including 11,808 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 0.22 ( 2117 hom., cov: 25)

Exomes 𝑓: 0.22 ( 9691 hom. )

Consequence

GABARAPL3
NR_028287.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.53

Publications

8 publications found

Variant links:

COSMIC-nc: COSV107448943

Genes affected

GABARAPL3 (HGNC:):

GABARAPL3 links:

GABARAPL3 (HGNC:4069): (GABA type A receptor associated protein like 3 (pseudogene)) Predicted to enable GABA receptor binding activity and ubiquitin protein ligase binding activity. Predicted to be involved in autophagosome assembly; autophagy of mitochondrion; and cellular response to nitrogen starvation. Predicted to be located in cytoplasmic vesicle and microtubule. Predicted to be active in autophagosome membrane and cytosol. [provided by Alliance of Genome Resources, Apr 2022]

GABARAPL3 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=-1.03).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_028287.1. 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
	GABARAPL3	NR_028287.1		n.698T>C		non_coding_transcript_exon	Exon 1 of 2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
GABARAPL3	ENST00000624044.1	TSL:6	n.1164A>G	non_coding_transcript_exon	Exon 1 of 1
ENSG00000310490	ENST00000850385.1		n.126+134T>C	intron	N/A
GABARAPL3	ENST00000412799.3	TSL:6	n.*94T>C	downstream_gene	N/A

Frequencies

GnomAD3 genomes

AF:

0.222

AC:

23638

AN:

106352

Hom.:

2116

Cov.:

show subpopulations

Gnomad AFR

AF:

0.129

Gnomad AMI

AF:

0.288

Gnomad AMR

AF:

0.167

Gnomad ASJ

AF:

0.273

Gnomad EAS

AF:

0.300

Gnomad SAS

AF:

0.305

Gnomad FIN

AF:

0.219

Gnomad MID

AF:

0.345

Gnomad NFE

AF:

0.265

Gnomad OTH

AF:

0.241

GnomAD4 exome

AF:

0.218

AC:

101156

AN:

463096

Hom.:

9691

Cov.:

AF XY:

0.225

AC XY:

56413

AN XY:

250396

show subpopulations

African (AFR)

AF:

0.0905

AC:

1100

AN:

12148

American (AMR)

AF:

0.114

AC:

2526

AN:

22154

Ashkenazi Jewish (ASJ)

AF:

0.214

AC:

3168

AN:

14786

East Asian (EAS)

AF:

0.240

AC:

7625

AN:

31784

South Asian (SAS)

AF:

0.309

AC:

14818

AN:

47938

European-Finnish (FIN)

AF:

0.195

AC:

6790

AN:

34786

Middle Eastern (MID)

AF:

0.216

AC:

659

AN:

3048

European-Non Finnish (NFE)

AF:

0.218

AC:

59077

AN:

270728

Other (OTH)

AF:

0.210

AC:

5393

AN:

25724

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

4117

8233

12350

16466

20583

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

388

776

1164

1552

1940

<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:

0.222

AC:

23631

AN:

106456

Hom.:

2117

Cov.:

AF XY:

0.220

AC XY:

11555

AN XY:

52528

show subpopulations

African (AFR)

AF:

0.128

AC:

3219

AN:

25106

American (AMR)

AF:

0.166

AC:

1795

AN:

10782

Ashkenazi Jewish (ASJ)

AF:

0.273

AC:

686

AN:

2514

East Asian (EAS)

AF:

0.300

AC:

1163

AN:

3882

South Asian (SAS)

AF:

0.305

AC:

1107

AN:

3630

European-Finnish (FIN)

AF:

0.219

AC:

1832

AN:

8364

Middle Eastern (MID)

AF:

0.337

AC:

AN:

190

European-Non Finnish (NFE)

AF:

0.265

AC:

13226

AN:

49886

Other (OTH)

AF:

0.242

AC:

349

AN:

1442

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.539

Heterozygous variant carriers

945

1890

2834

3779

4724

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

278

556

834

1112

1390

<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:

0.172

Hom.:

3185

Bravo

AF:

0.147

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.59

(source)

DANN

Benign

0.61

PhyloP100

-1.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over