1-182382098-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001033044.4(GLUL):c.*2307C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 152,068 control chromosomes in the GnomAD database, including 31,480 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.62 (31480 hom., cov: 32)
  • Exomes 𝑓: 0.38 (0 hom.)
• Consequence: GLUL NM_001033044.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0760

Genes affected

GLUL (HGNC:4341): (glutamate-ammonia ligase) The protein encoded by this gene belongs to the glutamine synthetase family. It catalyzes the synthesis of glutamine from glutamate and ammonia in an ATP-dependent reaction. This protein plays a role in ammonia and glutamate detoxification, acid-base homeostasis, cell signaling, and cell proliferation. Glutamine is an abundant amino acid, and is important to the biosynthesis of several amino acids, pyrimidines, and purines. Mutations in this gene are associated with congenital glutamine deficiency, and overexpression of this gene was observed in some primary liver cancer samples. There are six pseudogenes of this gene found on chromosomes 2, 5, 9, 11, and 12. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 1-182382098-G-A is Benign according to our data. Variant chr1-182382098-G-A is described in ClinVar as [Benign]. Clinvar id is 293891.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLUL	NM_001033044.4	c.*2307C>T		3_prime_UTR_variant	7/7	ENST00000331872.11
GLUL	NM_001033056.4	c.*2307C>T		3_prime_UTR_variant	7/7
GLUL	NM_002065.7	c.*2307C>T		3_prime_UTR_variant	8/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GLUL	ENST00000331872.11	c.*2307C>T		3_prime_UTR_variant	7/7	1	NM_001033044.4	P1
GLUL	ENST00000311223.9	c.*2307C>T		3_prime_UTR_variant	8/8	1		P1
GLUL	ENST00000417584.6	c.*2307C>T		3_prime_UTR_variant	7/7	5		P1
GLUL	ENST00000642379.1	c.*2307C>T		3_prime_UTR_variant	8/8

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94954 AN: 151942 Hom.: 31441 Cov.: 32

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.608

GnomAD4 exome AF: 0.375 AC: 3 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.333 AC XY: 2 AN XY: 6

Gnomad4 NFE exome AF: 0.375

GnomAD4 genome AF: 0.625 AC: 95037 AN: 152060 Hom.: 31480 Cov.: 32 AF XY: 0.623 AC XY: 46264 AN XY: 74308

Gnomad4 AFR AF: 0.848

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.832

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.606

Alfa AF: 0.553 Hom.: 2947

Bravo AF: 0.642

Asia WGS AF: 0.700 AC: 2435 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Congenital brain dysgenesis due to glutamine synthetase deficiency Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.0
Dann	Benign	0.47
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

Publications

LitVar

Other links and lift over

dbSNP: rs2296521; hg19: chr1-182351233;