NM_007278.2:c.*179T>A

Variant names:

• chr17-7240675-A-T
• rs17710
• NM_007278.2:c.*179T>A

Variant summary

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

The NM_007278.2(GABARAP):​c.*179T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 579,132 control chromosomes in the GnomAD database, including 5,701 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 0.11 (1101 hom., cov: 32)
  • Exomes 𝑓: 0.14 (4600 hom.)
• Consequence: GABARAP NM_007278.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.368
• Publications: 14 publications found

Genes affected

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]

ENSG00000262526 (HGNC:):

PHF23 (HGNC:28428): (PHD finger protein 23) Predicted to enable metal ion binding activity. Involved in negative regulation of autophagosome assembly; negative regulation of autophagosome maturation; and positive regulation of protein ubiquitination. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007278.2. 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.*179T>A		3_prime_UTR	Exon 4 of 4	NP_009209.1	Q6IAW1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABARAP	ENST00000302386.10	TSL:1 MANE Select	c.*179T>A		3_prime_UTR	Exon 4 of 4	ENSP00000306866.5	O95166
	ENSG00000262526	ENST00000570760.2	TSL:3	n.*439T>A		non_coding_transcript_exon	Exon 4 of 4	ENSP00000466023.1	I3L401
	ENSG00000262526	ENST00000570760.2	TSL:3	n.*439T>A		3_prime_UTR	Exon 4 of 4	ENSP00000466023.1	I3L401

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15990 AN: 152076 Hom.: 1098 Cov.: 32

Gnomad AFR AF: 0.0238

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.0705

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.0429

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.108

GnomAD4 exome AF: 0.136 AC: 58147 AN: 426938 Hom.: 4600 Cov.: 3 AF XY: 0.141 AC XY: 31815 AN XY: 226296

African (AFR) AF: 0.0224 AC: 263 AN: 11754

American (AMR) AF: 0.0578 AC: 953 AN: 16474

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 1670 AN: 12742

East Asian (EAS) AF: 0.0439 AC: 1290 AN: 29386

South Asian (SAS) AF: 0.211 AC: 9083 AN: 42978

European-Finnish (FIN) AF: 0.190 AC: 6029 AN: 31664

Middle Eastern (MID) AF: 0.133 AC: 292 AN: 2188

European-Non Finnish (NFE) AF: 0.139 AC: 35546 AN: 255208

Other (OTH) AF: 0.123 AC: 3021 AN: 24544

GnomAD4 genome AF: 0.105 AC: 15989 AN: 152194 Hom.: 1101 Cov.: 32 AF XY: 0.109 AC XY: 8093 AN XY: 74408

African (AFR) AF: 0.0237 AC: 986 AN: 41538

American (AMR) AF: 0.0704 AC: 1076 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 434 AN: 3470

East Asian (EAS) AF: 0.0426 AC: 221 AN: 5186

South Asian (SAS) AF: 0.211 AC: 1016 AN: 4826

European-Finnish (FIN) AF: 0.202 AC: 2139 AN: 10582

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9726 AN: 67986

Other (OTH) AF: 0.107 AC: 226 AN: 2112

Alfa AF: 0.132 Hom.: 186

Bravo AF: 0.0877

Asia WGS AF: 0.108 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.7
DANN	Benign	0.61
PhyloP100		0.37
Mutation Taster		=100/0	polymorphism (auto)

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: rs17710; hg19: chr17-7143994;