17-7242662-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000570760.2(ENSG00000262526):​n.84-983A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 376,770 control chromosomes in the GnomAD database, including 21,885 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 0.30 (7586 hom., cov: 33)
  • Exomes 𝑓: 0.35 (14299 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000570760.2. 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
	GABARAP	NM_007278.2	MANE Select	c.-332A>G		upstream_gene	N/A	NP_009209.1	Q6IAW1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000262526	ENST00000570760.2	TSL:3	n.84-983A>G		intron	N/A	ENSP00000466023.1	I3L401
	ENSG00000279641	ENST00000624722.1	TSL:6	n.463T>C		non_coding_transcript_exon	Exon 1 of 1
	GABARAP	ENST00000302386.10	TSL:1 MANE Select	c.-332A>G		upstream_gene	N/A	ENSP00000306866.5	O95166

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45763 AN: 152054 Hom.: 7594 Cov.: 33

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.301

GnomAD4 exome AF: 0.350 AC: 78528 AN: 224598 Hom.: 14299 Cov.: 0 AF XY: 0.348 AC XY: 41276 AN XY: 118656

African (AFR) AF: 0.146 AC: 828 AN: 5682

American (AMR) AF: 0.393 AC: 2430 AN: 6178

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 2451 AN: 7032

East Asian (EAS) AF: 0.350 AC: 3906 AN: 11174

South Asian (SAS) AF: 0.338 AC: 9883 AN: 29278

European-Finnish (FIN) AF: 0.333 AC: 4620 AN: 13854

Middle Eastern (MID) AF: 0.240 AC: 242 AN: 1008

European-Non Finnish (NFE) AF: 0.362 AC: 49594 AN: 137090

Other (OTH) AF: 0.344 AC: 4574 AN: 13302

GnomAD4 genome AF: 0.301 AC: 45745 AN: 152172 Hom.: 7586 Cov.: 33 AF XY: 0.299 AC XY: 22251 AN XY: 74390

African (AFR) AF: 0.152 AC: 6309 AN: 41532

American (AMR) AF: 0.351 AC: 5360 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1276 AN: 3472

East Asian (EAS) AF: 0.339 AC: 1749 AN: 5162

South Asian (SAS) AF: 0.326 AC: 1575 AN: 4824

European-Finnish (FIN) AF: 0.320 AC: 3395 AN: 10598

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 25025 AN: 67984

Other (OTH) AF: 0.297 AC: 628 AN: 2114

Alfa AF: 0.333 Hom.: 18183

Bravo AF: 0.298

Asia WGS AF: 0.298 AC: 1037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.7
DANN	Benign	0.51
PhyloP100		0.0020
PromoterAI		-0.0038	Neutral
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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;