1-32775688-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_003680.4(YARS1):​c.*293A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0362 in 453,694 control chromosomes in the GnomAD database, including 404 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.045 ( 187 hom., cov: 32)
Exomes 𝑓: 0.032 ( 217 hom. )

Consequence

YARS1
NM_003680.4 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.129
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 1-32775688-T-C is Benign according to our data. Variant chr1-32775688-T-C is described in ClinVar as [Benign]. Clinvar id is 297144.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0742 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
YARS1NM_003680.4 linkuse as main transcriptc.*293A>G 3_prime_UTR_variant 13/13 ENST00000373477.9 NP_003671.1
YARS1XM_011542347.3 linkuse as main transcriptc.*293A>G 3_prime_UTR_variant 11/11 XP_011540649.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
YARS1ENST00000373477.9 linkuse as main transcriptc.*293A>G 3_prime_UTR_variant 13/131 NM_003680.4 ENSP00000362576 P1

Frequencies

GnomAD3 genomes
AF:
0.0451
AC:
6865
AN:
152128
Hom.:
188
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0766
Gnomad AMI
AF:
0.0296
Gnomad AMR
AF:
0.0366
Gnomad ASJ
AF:
0.0781
Gnomad EAS
AF:
0.000385
Gnomad SAS
AF:
0.00724
Gnomad FIN
AF:
0.0206
Gnomad MID
AF:
0.0696
Gnomad NFE
AF:
0.0363
Gnomad OTH
AF:
0.0446
GnomAD4 exome
AF:
0.0317
AC:
9554
AN:
301448
Hom.:
217
Cov.:
0
AF XY:
0.0308
AC XY:
4832
AN XY:
156962
show subpopulations
Gnomad4 AFR exome
AF:
0.0755
Gnomad4 AMR exome
AF:
0.0277
Gnomad4 ASJ exome
AF:
0.0733
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00833
Gnomad4 FIN exome
AF:
0.0221
Gnomad4 NFE exome
AF:
0.0351
Gnomad4 OTH exome
AF:
0.0374
GnomAD4 genome
AF:
0.0451
AC:
6869
AN:
152246
Hom.:
187
Cov.:
32
AF XY:
0.0423
AC XY:
3148
AN XY:
74440
show subpopulations
Gnomad4 AFR
AF:
0.0765
Gnomad4 AMR
AF:
0.0366
Gnomad4 ASJ
AF:
0.0781
Gnomad4 EAS
AF:
0.000386
Gnomad4 SAS
AF:
0.00725
Gnomad4 FIN
AF:
0.0206
Gnomad4 NFE
AF:
0.0363
Gnomad4 OTH
AF:
0.0441
Alfa
AF:
0.0402
Hom.:
134
Bravo
AF:
0.0474
Asia WGS
AF:
0.0100
AC:
36
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingGeneDxJun 16, 2018- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Charcot-Marie-Tooth disease dominant intermediate C Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 12, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
11
DANN
Benign
0.65

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs16866009; hg19: chr1-33241289; API