chr1-32775529-CCCTTT-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_003680.4(YARS1):c.*447_*451del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00946 in 179,400 control chromosomes in the GnomAD database, including 18 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0092 ( 12 hom., cov: 32)
Exomes 𝑓: 0.011 ( 6 hom. )
Consequence
YARS1
NM_003680.4 3_prime_UTR
NM_003680.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.62
Genes affected
YARS1 (HGNC:12840): (tyrosyl-tRNA synthetase 1) Aminoacyl-tRNA synthetases catalyze the aminoacylation of tRNA by their cognate amino acid. Because of their central role in linking amino acids with nucleotide triplets contained in tRNAs, aminoacyl-tRNA synthetases are thought to be among the first proteins that appeared in evolution. Tyrosyl-tRNA synthetase belongs to the class I tRNA synthetase family. Cytokine activities have also been observed for the human tyrosyl-tRNA synthetase, after it is split into two parts, an N-terminal fragment that harbors the catalytic site and a C-terminal fragment found only in the mammalian enzyme. The N-terminal fragment is an interleukin-8-like cytokine, whereas the released C-terminal fragment is an EMAP II-like cytokine. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 1-32775529-CCCTTT-C is Benign according to our data. Variant chr1-32775529-CCCTTT-C is described in ClinVar as [Likely_benign]. Clinvar id is 297138.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00923 (1405/152298) while in subpopulation SAS AF= 0.0325 (157/4826). AF 95% confidence interval is 0.0284. There are 12 homozygotes in gnomad4. There are 762 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 12 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YARS1 | NM_003680.4 | c.*447_*451del | 3_prime_UTR_variant | 13/13 | ENST00000373477.9 | ||
YARS1 | XM_011542347.3 | c.*447_*451del | 3_prime_UTR_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YARS1 | ENST00000373477.9 | c.*447_*451del | 3_prime_UTR_variant | 13/13 | 1 | NM_003680.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00922 AC: 1403AN: 152180Hom.: 12 Cov.: 32
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GnomAD4 exome AF: 0.0108 AC: 293AN: 27102Hom.: 6 AF XY: 0.0131 AC XY: 186AN XY: 14172
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GnomAD4 genome ? AF: 0.00923 AC: 1405AN: 152298Hom.: 12 Cov.: 32 AF XY: 0.0102 AC XY: 762AN XY: 74476
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Charcot-Marie-Tooth, Intermediate Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at