17-3476008-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_000049.4(ASPA):c.-152C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000952 in 714,124 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000099 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000094 ( 0 hom. )
Consequence
ASPA
NM_000049.4 5_prime_UTR
NM_000049.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.310
Publications
0 publications found
Genes affected
ASPA (HGNC:756): (aspartoacylase) This gene encodes an enzyme that catalyzes the conversion of N-acetyl_L-aspartic acid (NAA) to aspartate and acetate. NAA is abundant in the brain where hydrolysis by aspartoacylase is thought to help maintain white matter. This protein is an NAA scavenger in other tissues. Mutations in this gene cause Canavan disease. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]
SPATA22 (HGNC:30705): (spermatogenesis associated 22) Predicted to be involved in regulation of meiotic cell cycle. Predicted to act upstream of or within several processes, including fertilization; gamete generation; and meiosis I cell cycle process. Predicted to be located in chromosome. [provided by Alliance of Genome Resources, Apr 2022]
SPATA22 Gene-Disease associations (from GenCC):
- infertility disorderInheritance: AR Classification: MODERATE Submitted by: Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152148Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
15
AN:
152148
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:
GnomAD4 exome AF: 0.0000943 AC: 53AN: 561858Hom.: 0 Cov.: 8 AF XY: 0.0000809 AC XY: 24AN XY: 296704 show subpopulations
GnomAD4 exome
AF:
AC:
53
AN:
561858
Hom.:
Cov.:
8
AF XY:
AC XY:
24
AN XY:
296704
show subpopulations
African (AFR)
AF:
AC:
0
AN:
14624
American (AMR)
AF:
AC:
0
AN:
23550
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
16162
East Asian (EAS)
AF:
AC:
48
AN:
31836
South Asian (SAS)
AF:
AC:
2
AN:
51108
European-Finnish (FIN)
AF:
AC:
0
AN:
30728
Middle Eastern (MID)
AF:
AC:
0
AN:
2290
European-Non Finnish (NFE)
AF:
AC:
0
AN:
361530
Other (OTH)
AF:
AC:
3
AN:
30030
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
4
7
11
14
18
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152266Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74448 show subpopulations
GnomAD4 genome
AF:
AC:
15
AN:
152266
Hom.:
Cov.:
32
AF XY:
AC XY:
9
AN XY:
74448
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41552
American (AMR)
AF:
AC:
1
AN:
15300
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
14
AN:
5182
South Asian (SAS)
AF:
AC:
0
AN:
4822
European-Finnish (FIN)
AF:
AC:
0
AN:
10622
Middle Eastern (MID)
AF:
AC:
0
AN:
292
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68000
Other (OTH)
AF:
AC:
0
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Spongy degeneration of central nervous system Uncertain:1
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance:Uncertain significance
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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