15-90348750-A-T

Variant names:

• chr15-90348750-A-T
• rs3803539
• ENST00000624044.1:n.1164A>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000624044.1(GABARAPL3):​n.1164A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.0062 (0 hom., cov: 25)
  • Exomes 𝑓: 0.039 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GABARAPL3 ENST00000624044.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 8 publications found

Genes affected

GABARAPL3 (HGNC:):

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]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GABARAPL3	NR_028287.1	n.698T>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GABARAPL3	ENST00000624044.1	n.1164A>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000310490	ENST00000850385.1	n.126+134T>A		intron_variant	Intron 1 of 1
GABARAPL3	ENST00000412799.3	n.*94T>A		downstream_gene_variant		6
ENSG00000310483	ENST00000850324.1	n.*56A>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.00626 AC: 637 AN: 101830 Hom.: 0 Cov.: 25

Gnomad AFR AF: 0.0101

Gnomad AMI AF: 0.00314

Gnomad AMR AF: 0.00483

Gnomad ASJ AF: 0.0109

Gnomad EAS AF: 0.00862

Gnomad SAS AF: 0.00762

Gnomad FIN AF: 0.00267

Gnomad MID AF: 0.00485

Gnomad NFE AF: 0.00487

Gnomad OTH AF: 0.00441

GnomAD4 exome AF: 0.0392 AC: 17371 AN: 442636 Hom.: 0 Cov.: 4 AF XY: 0.0364 AC XY: 8711 AN XY: 239382

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0409 AC: 469 AN: 11460

American (AMR) AF: 0.0591 AC: 1243 AN: 21040

Ashkenazi Jewish (ASJ) AF: 0.0296 AC: 424 AN: 14342

East Asian (EAS) AF: 0.0222 AC: 689 AN: 31046

South Asian (SAS) AF: 0.0479 AC: 2131 AN: 44474

European-Finnish (FIN) AF: 0.0175 AC: 594 AN: 33870

Middle Eastern (MID) AF: 0.0168 AC: 50 AN: 2976

European-Non Finnish (NFE) AF: 0.0421 AC: 10891 AN: 258676

Other (OTH) AF: 0.0356 AC: 880 AN: 24752

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00624 AC: 636 AN: 101932 Hom.: 0 Cov.: 25 AF XY: 0.00610 AC XY: 308 AN XY: 50474

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0101 AC: 237 AN: 23512

American (AMR) AF: 0.00483 AC: 50 AN: 10356

Ashkenazi Jewish (ASJ) AF: 0.0109 AC: 26 AN: 2392

East Asian (EAS) AF: 0.00864 AC: 32 AN: 3702

South Asian (SAS) AF: 0.00735 AC: 26 AN: 3536

European-Finnish (FIN) AF: 0.00267 AC: 22 AN: 8232

Middle Eastern (MID) AF: 0.00526 AC: 1 AN: 190

European-Non Finnish (NFE) AF: 0.00488 AC: 234 AN: 47996

Other (OTH) AF: 0.00435 AC: 6 AN: 1380

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.000133 Hom.: 3185

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.50
DANN	Benign	0.81
PhyloP100		-1.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3803539; hg19: chr15-90891982;