dbSNP rs11541416: TARS1:p.Val118Ile (chr5-33453311-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_152295.5(TARS1):c.352G>A(p.Val118Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00107 in 1,546,276 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0061 ( 8 hom., cov: 29)

Exomes 𝑓: 0.00059 ( 8 hom. )

Consequence

TARS1
NM_152295.5 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 6.85

Publications

3 publications found

Variant links:

Genes affected

TARS1 (HGNC:11572): (threonyl-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. Threonyl-tRNA synthetase belongs to the class-II aminoacyl-tRNA synthetase family [provided by RefSeq, Jul 2008]

TARS1 Gene-Disease associations (from GenCC):

trichothiodystrophy 7, nonphotosensitive
Inheritance: AR Classification: STRONG Submitted by: G2P
trichothiodystrophy
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

TARS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.006256461).

BP6

Variant 5-33453311-G-A is Benign according to our data. Variant chr5-33453311-G-A is described in ClinVar as Benign. ClinVar VariationId is 716827.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00614 (825/134256) while in subpopulation AFR AF = 0.0219 (776/35384). AF 95% confidence interval is 0.0207. There are 8 homozygotes in GnomAd4. There are 362 alleles in the male GnomAd4 subpopulation. Median coverage is 29. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 8 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152295.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
TARS1	NM_152295.5	MANE Select	c.352G>A	p.Val118Ile	missense	Exon 4 of 19	NP_689508.3
TARS1	NM_001258438.2		c.451G>A	p.Val151Ile	missense	Exon 5 of 20	NP_001245367.1
TARS1	NM_001258437.1		c.352G>A	p.Val118Ile	missense	Exon 5 of 20	NP_001245366.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
TARS1	ENST00000265112.8	TSL:1 MANE Select	c.352G>A	p.Val118Ile	missense	Exon 4 of 19	ENSP00000265112.3
TARS1	ENST00000509731.5	TSL:1	n.*305G>A		non_coding_transcript_exon	Exon 5 of 19	ENSP00000427304.1
TARS1	ENST00000509731.5	TSL:1	n.*305G>A		3_prime_UTR	Exon 5 of 19	ENSP00000427304.1

Frequencies

GnomAD3 genomes

AF:

0.00610

AC:

818

AN:

134198

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0218

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00293

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000438

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000766

Gnomad OTH

AF:

0.00394

GnomAD2 exomes

AF:

0.00152

AC:

366

AN:

240640

AF XY:

0.00104

show subpopulations

Gnomad AFR exome

AF:

0.0197

Gnomad AMR exome

AF:

0.00122

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000175

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000119

Gnomad OTH exome

AF:

0.000864

GnomAD4 exome

AF:

0.000591

AC:

834

AN:

1412020

Hom.:

Cov.:

AF XY:

0.000535

AC XY:

375

AN XY:

701528

show subpopulations

African (AFR)

AF:

0.0201

AC:

644

AN:

32050

American (AMR)

AF:

0.00123

AC:

AN:

42326

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

24902

East Asian (EAS)

AF:

0.000161

AC:

AN:

37174

South Asian (SAS)

AF:

0.0000374

AC:

AN:

80300

European-Finnish (FIN)

AF:

0.00

AC:

AN:

50712

Middle Eastern (MID)

AF:

0.00155

AC:

AN:

5156

European-Non Finnish (NFE)

AF:

0.0000435

AC:

AN:

1081588

Other (OTH)

AF:

0.00128

AC:

AN:

57812

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.466

Heterozygous variant carriers

115

153

191

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00614

AC:

825

AN:

134256

Hom.:

Cov.:

AF XY:

0.00569

AC XY:

362

AN XY:

63624

show subpopulations

African (AFR)

AF:

0.0219

AC:

776

AN:

35384

American (AMR)

AF:

0.00293

AC:

AN:

11942

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3396

East Asian (EAS)

AF:

0.000439

AC:

AN:

4556

South Asian (SAS)

AF:

0.00

AC:

AN:

4228

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6598

Middle Eastern (MID)

AF:

0.00

AC:

AN:

216

European-Non Finnish (NFE)

AF:

0.0000766

AC:

AN:

65272

Other (OTH)

AF:

0.00393

AC:

AN:

1780

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

115

154

192

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0214

Hom.:

2357

Bravo

AF:

0.00666

ESP6500AA

AF:

0.0200

AC:

ESP6500EA

AF:

0.000349

AC:

ExAC

AF:

0.00171

AC:

208

Asia WGS

AF:

0.00173

AC:

AN:

3478

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

TARS1-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.088

BayesDel_addAF

Benign

-0.51

BayesDel_noAF

Benign

-0.43

CADD

Benign

(source)

DANN

Benign

0.97

DEOGEN2

Benign

0.0086

Eigen

Benign

-0.17

Eigen_PC

Benign

-0.10

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Benign

0.39

MetaRNN

Benign

0.0063

PhyloP100

6.9

Sift4G

Benign

0.087

Vest4

0.39

MVP

0.53

ClinPred

0.051

GERP RS

4.1

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.057

Mutation Taster

=94/6

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over