NM_004446.3:c.2182-1102C>T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004446.3(EPRS1):c.2182-1102C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 152,052 control chromosomes in the GnomAD database, including 49,087 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 0.80 ( 49087 hom., cov: 31)
Consequence
EPRS1
NM_004446.3 intron
NM_004446.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.313
Publications
4 publications found
Genes affected
EPRS1 (HGNC:3418): (glutamyl-prolyl-tRNA synthetase 1) Aminoacyl-tRNA synthetases are a class of enzymes that charge tRNAs with their cognate amino acids. The protein encoded by this gene is a multifunctional aminoacyl-tRNA synthetase that catalyzes the aminoacylation of glutamic acid and proline tRNA species. Alternative splicing has been observed for this gene, but the full-length nature and biological validity of the variant have not been determined. [provided by RefSeq, Jul 2008]
EPRS1 Gene-Disease associations (from GenCC):
- leukodystrophy, hypomyelinating, 15Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
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=-1.02).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EPRS1 | ENST00000366923.8 | c.2182-1102C>T | intron_variant | Intron 17 of 31 | 1 | NM_004446.3 | ENSP00000355890.3 | |||
EPRS1 | ENST00000609181.5 | c.2203-1102C>T | intron_variant | Intron 18 of 20 | 1 | ENSP00000477245.1 | ||||
EPRS1 | ENST00000464052.5 | n.604-1102C>T | intron_variant | Intron 4 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.802 AC: 121878AN: 151934Hom.: 49048 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
121878
AN:
151934
Hom.:
Cov.:
31
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: 0.802 AC: 121971AN: 152052Hom.: 49087 Cov.: 31 AF XY: 0.804 AC XY: 59739AN XY: 74310 show subpopulations
GnomAD4 genome
AF:
AC:
121971
AN:
152052
Hom.:
Cov.:
31
AF XY:
AC XY:
59739
AN XY:
74310
show subpopulations
African (AFR)
AF:
AC:
31534
AN:
41438
American (AMR)
AF:
AC:
12969
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
AC:
2501
AN:
3470
East Asian (EAS)
AF:
AC:
4814
AN:
5182
South Asian (SAS)
AF:
AC:
4022
AN:
4814
European-Finnish (FIN)
AF:
AC:
8623
AN:
10550
Middle Eastern (MID)
AF:
AC:
226
AN:
292
European-Non Finnish (NFE)
AF:
AC:
54893
AN:
67996
Other (OTH)
AF:
AC:
1682
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1221
2443
3664
4886
6107
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
878
1756
2634
3512
4390
<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:
3089
AN:
3476
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
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