rs228773
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_153006.3(NAGS):c.1451+9T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 29)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
NAGS
NM_153006.3 intron
NM_153006.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.80
Genes affected
NAGS (HGNC:17996): (N-acetylglutamate synthase) The N-acetylglutamate synthase gene encodes a mitochondrial enzyme that catalyzes the formation of N-acetylglutamate (NAG) from glutamate and acetyl coenzyme-A. NAG is a cofactor of carbamyl phosphate synthetase I (CPSI), the first enzyme of the urea cycle in mammals. This gene may regulate ureagenesis by altering NAG availability and, thereby, CPSI activity. Deficiencies in N-acetylglutamate synthase have been associated with hyperammonemia. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
?
Variant 17-44007782-T-A is Benign according to our data. Variant chr17-44007782-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 2857799.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAGS | NM_153006.3 | c.1451+9T>A | intron_variant | ENST00000293404.8 | |||
NAGS | XM_011524438.2 | c.1268+288T>A | intron_variant | ||||
NAGS | XM_011524439.2 | c.953+9T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAGS | ENST00000293404.8 | c.1451+9T>A | intron_variant | 1 | NM_153006.3 | P1 | |||
NAGS | ENST00000589767.1 | c.1382+9T>A | intron_variant | 2 | |||||
NAGS | ENST00000592915.1 | n.1339+9T>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 29
GnomAD3 genomes
?
Cov.:
29
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1421334Hom.: 0 Cov.: 51 AF XY: 0.00 AC XY: 0AN XY: 703380
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1421334
Hom.:
Cov.:
51
AF XY:
AC XY:
0
AN XY:
703380
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 29
GnomAD4 genome
?
Cov.:
29
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hyperammonemia, type III Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 19, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at