rs222843

Variant names:

• chr17-7242662-T-A
• rs222843
• ENST00000570760.2:n.84-983A>T

Your query was ambiguous. Multiple possible variants found:

• chr17-7242662-T-A
• chr17-7242662-T-C
• chr17-7242662-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000570760.2(ENSG00000262526):​n.84-983A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000262526 ENST00000570760.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 33 publications found

Genes affected

ENSG00000262526 (HGNC:):

GABARAP (HGNC:4067): (GABA type A receptor-associated protein) Gamma-aminobutyric acid A receptors [GABA(A) receptors] are ligand-gated chloride channels that mediate inhibitory neurotransmission. This gene encodes GABA(A) receptor-associated protein, which is highly positively charged in its N-terminus and shares sequence similarity with light chain-3 of microtubule-associated proteins 1A and 1B. This protein clusters neurotransmitter receptors by mediating interaction with the cytoskeleton. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GABARAP	NM_007278.2	c.-332A>T		upstream_gene_variant		ENST00000302386.10	NP_009209.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000262526	ENST00000570760.2	n.84-983A>T		intron_variant	Intron 1 of 3	3		ENSP00000466023.1
ENSG00000279641	ENST00000624722.1	n.463T>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
GABARAP	ENST00000302386.10	c.-332A>T		upstream_gene_variant		1	NM_007278.2	ENSP00000306866.5
GABARAP	ENST00000573928.1	c.-332A>T		upstream_gene_variant		1		ENSP00000458476.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 225300 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 119028

African (AFR) AF: 0.00 AC: 0 AN: 5696

American (AMR) AF: 0.00 AC: 0 AN: 6196

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 7050

East Asian (EAS) AF: 0.00 AC: 0 AN: 11224

South Asian (SAS) AF: 0.00 AC: 0 AN: 29328

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 13886

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1012

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 137572

Other (OTH) AF: 0.00 AC: 0 AN: 13336

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.1
DANN	Benign	0.72
PhyloP100		0.0020
PromoterAI		0.013	Neutral

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: rs222843; hg19: chr17-7145981;