GeneBe

rs57674096

Variant names:

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS1

The NM_014905.5(GLS):​c.-203_-165delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000942 in 743,090 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000084 ( 0 hom. )

Consequence

GLS
NM_014905.5 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.335
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS1
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.00000842 (5/593578) while in subpopulation AMR AF= 0.0000643 (2/31118). AF 95% confidence interval is 0.0000106. There are 0 homozygotes in gnomad4_exome. There are 4 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GLSNM_014905.5 linkc.-203_-165delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA 5_prime_UTR_variant Exon 1 of 18 ENST00000320717.8 NP_055720.3 O94925-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GLSENST00000320717 linkc.-203_-165delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA 5_prime_UTR_variant Exon 1 of 18 1 NM_014905.5 ENSP00000317379.3 O94925-1
GLSENST00000338435 linkc.-203_-165delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA 5_prime_UTR_variant Exon 1 of 15 1 ENSP00000340689.4 O94925-3
GLSENST00000479552.1 linkn.11_49delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA non_coding_transcript_exon_variant Exon 1 of 2 1
ENSG00000235852ENST00000413911.1 linkn.805_843delTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC non_coding_transcript_exon_variant Exon 2 of 2 3

Frequencies

GnomAD3 genomes
AF:
0.0000134
AC:
2
AN:
149512
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000201
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000149
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000842
AC:
5
AN:
593578
Hom.:
0
AF XY:
0.0000126
AC XY:
4
AN XY:
316268
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000643
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000798
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000134
AC:
2
AN:
149512
Hom.:
0
Cov.:
0
AF XY:
0.0000137
AC XY:
1
AN XY:
72816
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000201
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000149
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs57674096; hg19: chr2-191745598; API