rs2027735
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018696.3(ELAC1):c.157+4483C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,060 control chromosomes in the GnomAD database, including 10,679 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 0.37 ( 10679 hom., cov: 32)
Consequence
ELAC1
NM_018696.3 intron
NM_018696.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.00200
Genes affected
ELAC1 (HGNC:14197): (elaC ribonuclease Z 1) Predicted to enable 3'-tRNA processing endoribonuclease activity. Predicted to be involved in tRNA 3'-trailer cleavage, endonucleolytic. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELAC1 | NM_018696.3 | c.157+4483C>T | intron_variant | ENST00000269466.8 | |||
LOC107985152 | XR_007066371.1 | n.10777-4051G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELAC1 | ENST00000269466.8 | c.157+4483C>T | intron_variant | 1 | NM_018696.3 | P1 | |||
ELAC1 | ENST00000591429.1 | c.157+4483C>T | intron_variant | 1 | |||||
ELAC1 | ENST00000588577.5 | c.157+4483C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.372 AC: 56534AN: 151942Hom.: 10678 Cov.: 32
GnomAD3 genomes
?
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151942
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.372 AC: 56571AN: 152060Hom.: 10679 Cov.: 32 AF XY: 0.370 AC XY: 27528AN XY: 74338
GnomAD4 genome
?
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56571
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152060
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32
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27528
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74338
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1244
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
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