chr16-29687304-G-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014298.6(QPRT):c.14-7360G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 152,122 control chromosomes in the GnomAD database, including 6,724 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 0.29 ( 6724 hom., cov: 32)
Consequence
QPRT
NM_014298.6 intron
NM_014298.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.516
Publications
11 publications found
Genes affected
QPRT (HGNC:9755): (quinolinate phosphoribosyltransferase) This gene encodes a key enzyme in catabolism of quinolinate, an intermediate in the tryptophan-nicotinamide adenine dinucleotide pathway. Quinolinate acts as a most potent endogenous exitotoxin to neurons. Elevation of quinolinate levels in the brain has been linked to the pathogenesis of neurodegenerative disorders such as epilepsy, Alzheimer's disease, and Huntington's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
QPRT | ENST00000395384.9 | c.14-7360G>T | intron_variant | Intron 1 of 3 | 1 | NM_014298.6 | ENSP00000378782.4 | |||
QPRT | ENST00000449759.2 | c.14-7360G>T | intron_variant | Intron 2 of 4 | 3 | ENSP00000404873.3 | ||||
QPRT | ENST00000562473.1 | c.14-7360G>T | intron_variant | Intron 1 of 3 | 3 | ENSP00000455183.1 | ||||
QPRT | ENST00000219771.7 | n.203+8094G>T | intron_variant | Intron 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.287 AC: 43623AN: 152004Hom.: 6705 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
43623
AN:
152004
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.287 AC: 43677AN: 152122Hom.: 6724 Cov.: 32 AF XY: 0.282 AC XY: 20937AN XY: 74374 show subpopulations
GnomAD4 genome
AF:
AC:
43677
AN:
152122
Hom.:
Cov.:
32
AF XY:
AC XY:
20937
AN XY:
74374
show subpopulations
African (AFR)
AF:
AC:
16107
AN:
41478
American (AMR)
AF:
AC:
2911
AN:
15262
Ashkenazi Jewish (ASJ)
AF:
AC:
878
AN:
3470
East Asian (EAS)
AF:
AC:
606
AN:
5182
South Asian (SAS)
AF:
AC:
1027
AN:
4826
European-Finnish (FIN)
AF:
AC:
2873
AN:
10592
Middle Eastern (MID)
AF:
AC:
77
AN:
294
European-Non Finnish (NFE)
AF:
AC:
18263
AN:
67994
Other (OTH)
AF:
AC:
529
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
1583
3167
4750
6334
7917
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
438
876
1314
1752
2190
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
473
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.