rs3217036

Positions:

• chr2-190894951-AT-A
• chr2-190894951-AT-ATT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_014905.5(GLS):​c.387-193del variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.44 (18644 hom., cov: 0)
• Consequence: GLS NM_014905.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530

Genes affected

GLS (HGNC:4331): (glutaminase) This gene encodes the K-type mitochondrial glutaminase. The encoded protein is an phosphate-activated amidohydrolase that catalyzes the hydrolysis of glutamine to glutamate and ammonia. This protein is primarily expressed in the brain and kidney plays an essential role in generating energy for metabolism, synthesizing the brain neurotransmitter glutamate and maintaining acid-base balance in the kidney. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2012]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GLS	NM_014905.5	c.387-193del		intron_variant		ENST00000320717.8	NP_055720.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GLS	ENST00000320717.8	c.387-193del		intron_variant		1	NM_014905.5	ENSP00000317379	P1

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67409 AN: 151610 Hom.: 18639 Cov.: 0

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.453

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.444 AC: 67433 AN: 151728 Hom.: 18644 Cov.: 0 AF XY: 0.447 AC XY: 33125 AN XY: 74152

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.453

Alfa AF: 0.431 Hom.: 1602

Bravo AF: 0.410

Asia WGS AF: 0.351 AC: 1221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs3217036; hg19: chr2-191759677;