rs5030754
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1
The NM_004446.3(EPRS1):c.3102G>A(p.Lys1034=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.09 in 1,605,802 control chromosomes in the GnomAD database, including 7,694 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.12 ( 1366 hom., cov: 33)
Exomes 𝑓: 0.087 ( 6328 hom. )
Consequence
EPRS1
NM_004446.3 synonymous
NM_004446.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.05
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.24).
BP6
?
Variant 1-219983387-C-T is Benign according to our data. Variant chr1-219983387-C-T is described in ClinVar as [Benign]. Clinvar id is 1166607.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.05 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPRS1 | NM_004446.3 | c.3102G>A | p.Lys1034= | synonymous_variant | 22/32 | ENST00000366923.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPRS1 | ENST00000366923.8 | c.3102G>A | p.Lys1034= | synonymous_variant | 22/32 | 1 | NM_004446.3 | P1 | |
EPRS1 | ENST00000485821.1 | n.65G>A | non_coding_transcript_exon_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.119 AC: 18031AN: 152130Hom.: 1365 Cov.: 33
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GnomAD3 exomes AF: 0.0798 AC: 19772AN: 247864Hom.: 1014 AF XY: 0.0765 AC XY: 10240AN XY: 133838
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GnomAD4 exome AF: 0.0870 AC: 126456AN: 1453554Hom.: 6328 Cov.: 31 AF XY: 0.0849 AC XY: 61384AN XY: 723168
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GnomAD4 genome ? AF: 0.119 AC: 18066AN: 152248Hom.: 1366 Cov.: 33 AF XY: 0.113 AC XY: 8415AN XY: 74454
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
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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