chr2-72888868-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003124.5(SPR):c.595+264G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.836 in 152,200 control chromosomes in the GnomAD database, including 54,537 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.84 ( 54537 hom., cov: 32)
Consequence
SPR
NM_003124.5 intron
NM_003124.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.297
Publications
4 publications found
Genes affected
SPR (HGNC:11257): (sepiapterin reductase) This gene encodes an aldo-keto reductase that catalyzes the NADPH-dependent reduction of pteridine derivatives and is important in the biosynthesis of tetrahydrobiopterin (BH4). Mutations in this gene result in DOPA-responsive dystonia due to sepiaterin reductase deficiency. A pseudogene has been identified on chromosome 1. [provided by RefSeq, Jul 2008]
SPR Gene-Disease associations (from GenCC):
- dopa-responsive dystonia due to sepiapterin reductase deficiencyInheritance: AD, AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Genomics England PanelApp, Orphanet, ClinGen, G2P, Ambry Genetics
- BH4-deficient hyperphenylalaninemia AInheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 2-72888868-G-A is Benign according to our data. Variant chr2-72888868-G-A is described in CliVar as Benign. Clinvar id is 1280180.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-72888868-G-A is described in CliVar as Benign. Clinvar id is 1280180.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-72888868-G-A is described in CliVar as Benign. Clinvar id is 1280180.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-72888868-G-A is described in CliVar as Benign. Clinvar id is 1280180.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-72888868-G-A is described in CliVar as Benign. Clinvar id is 1280180.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-72888868-G-A is described in CliVar as Benign. Clinvar id is 1280180.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPR | ENST00000234454.6 | c.595+264G>A | intron_variant | Intron 2 of 2 | 1 | NM_003124.5 | ENSP00000234454.5 | |||
SPR | ENST00000713723.1 | c.304+1132G>A | intron_variant | Intron 1 of 1 | ENSP00000519027.1 | |||||
SPR | ENST00000498749.2 | n.*177+264G>A | intron_variant | Intron 2 of 2 | 3 | ENSP00000519026.1 |
Frequencies
GnomAD3 genomes AF: 0.837 AC: 127256AN: 152082Hom.: 54529 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
127256
AN:
152082
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: 0.836 AC: 127290AN: 152200Hom.: 54537 Cov.: 32 AF XY: 0.842 AC XY: 62654AN XY: 74420 show subpopulations
GnomAD4 genome
AF:
AC:
127290
AN:
152200
Hom.:
Cov.:
32
AF XY:
AC XY:
62654
AN XY:
74420
show subpopulations
African (AFR)
AF:
AC:
26230
AN:
41458
American (AMR)
AF:
AC:
13705
AN:
15306
Ashkenazi Jewish (ASJ)
AF:
AC:
3251
AN:
3472
East Asian (EAS)
AF:
AC:
5143
AN:
5182
South Asian (SAS)
AF:
AC:
4523
AN:
4826
European-Finnish (FIN)
AF:
AC:
10061
AN:
10626
Middle Eastern (MID)
AF:
AC:
265
AN:
294
European-Non Finnish (NFE)
AF:
AC:
61519
AN:
68016
Other (OTH)
AF:
AC:
1794
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
935
1871
2806
3742
4677
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
880
1760
2640
3520
4400
<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:
3215
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jun 26, 2018
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational 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
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