rs1365700579

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001040436.3(YARS2):ā€‹c.1106G>Cā€‹(p.Cys369Ser) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,878 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: š‘“ 0.000039 ( 0 hom., cov: 32)
Exomes š‘“: 0.0000014 ( 0 hom. )

Consequence

YARS2
NM_001040436.3 missense, splice_region

Scores

2
7
10

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.29
Variant links:
Genes affected
YARS2 (HGNC:24249): (tyrosyl-tRNA synthetase 2) This gene encodes a mitochondrial protein that catalyzes the attachment of tyrosine to tRNA(Tyr). Mutations in this gene are associated with myopathy with lactic acidosis and sideroblastic anemia type 2 (MLASA2). [provided by RefSeq, Jan 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
YARS2NM_001040436.3 linkuse as main transcriptc.1106G>C p.Cys369Ser missense_variant, splice_region_variant 4/5 ENST00000324868.13 NP_001035526.1 Q9Y2Z4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
YARS2ENST00000324868.13 linkuse as main transcriptc.1106G>C p.Cys369Ser missense_variant, splice_region_variant 4/51 NM_001040436.3 ENSP00000320658.8 Q9Y2Z4
YARS2ENST00000548490.1 linkuse as main transcriptn.*117G>C splice_region_variant, non_coding_transcript_exon_variant 4/55 ENSP00000447710.1 H0YHS6
YARS2ENST00000551673.5 linkuse as main transcriptn.3G>C non_coding_transcript_exon_variant 1/35
YARS2ENST00000548490.1 linkuse as main transcriptn.*117G>C 3_prime_UTR_variant 4/55 ENSP00000447710.1 H0YHS6

Frequencies

GnomAD3 genomes
AF:
0.0000394
AC:
6
AN:
152110
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000393
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00000796
AC:
2
AN:
251400
Hom.:
0
AF XY:
0.0000147
AC XY:
2
AN XY:
135882
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000578
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1461768
Hom.:
0
Cov.:
31
AF XY:
0.00000275
AC XY:
2
AN XY:
727180
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000447
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000394
AC:
6
AN:
152110
Hom.:
0
Cov.:
32
AF XY:
0.0000538
AC XY:
4
AN XY:
74298
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.000393
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.75
BayesDel_addAF
Uncertain
0.11
D
BayesDel_noAF
Uncertain
0.090
CADD
Uncertain
24
DANN
Benign
0.96
DEOGEN2
Benign
0.41
T
Eigen
Benign
0.12
Eigen_PC
Uncertain
0.32
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Benign
0.75
T
M_CAP
Benign
0.010
T
MetaRNN
Uncertain
0.44
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.4
L
PrimateAI
Uncertain
0.75
T
PROVEAN
Uncertain
-3.7
D
REVEL
Uncertain
0.35
Sift
Benign
0.097
T
Sift4G
Benign
0.14
T
Polyphen
0.021
B
Vest4
0.66
MutPred
0.62
Gain of disorder (P = 0.0037);
MVP
0.40
MPC
0.61
ClinPred
0.71
D
GERP RS
5.5
Varity_R
0.76
gMVP
0.63

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: rs1365700579; hg19: chr12-32903039; API