chr5-33453263-CTT-C

Variant names:

• chr5-33453263-CTT-C
• rs35931457
• NM_152295.5:c.330-5_330-4delTT

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP6 BS2

The NM_152295.5(TARS1):​c.330-5_330-4delTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0866 in 1,240,962 control chromosomes in the GnomAD database, including 17 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.0014 (0 hom., cov: 22)
  • Exomes 𝑓: 0.095 (17 hom.)
• Consequence: TARS1 NM_152295.5 splice_region, intron
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: 0.694
• Publications: 1 publications found

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, MODERATE Submitted by: PanelApp Australia, G2P
• trichothiodystrophy

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• BP6: Variant 5-33453263-CTT-C is Benign according to our data. Variant chr5-33453263-CTT-C is described in ClinVar as Likely_benign. ClinVar VariationId is 3055549.Status of the report is no_assertion_criteria_provided, 0 stars.
• BS2: High Homozygotes in GnomAdExome4 at 17 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TARS1	NM_152295.5	MANE Select	c.330-5_330-4delTT		splice_region intron	N/A	NP_689508.3
	TARS1	NM_001258438.2		c.429-5_429-4delTT		splice_region intron	N/A	NP_001245367.1	P26639-2
	TARS1	NM_001258437.1		c.330-5_330-4delTT		splice_region intron	N/A	NP_001245366.1	P26639-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TARS1	ENST00000265112.8	TSL:1 MANE Select	c.330-25_330-24delTT		intron	N/A	ENSP00000265112.3	P26639-1
	TARS1	ENST00000509731.5	TSL:1	n.*283-25_*283-24delTT		intron	N/A	ENSP00000427304.1	D6RJ97
	TARS1	ENST00000455217.6	TSL:2	c.429-25_429-24delTT		intron	N/A	ENSP00000387710.2	P26639-2

Frequencies

GnomAD3 genomes AF: 0.00136 AC: 143 AN: 105202 Hom.: 0 Cov.: 22

Gnomad AFR AF: 0.00349

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000840

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00136

Gnomad FIN AF: 0.00266

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000236

Gnomad OTH AF: 0.00216

GnomAD4 exome AF: 0.0945 AC: 107352 AN: 1135758 Hom.: 17 AF XY: 0.0964 AC XY: 53815 AN XY: 558080

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.118 AC: 2957 AN: 25002

American (AMR) AF: 0.105 AC: 2084 AN: 19852

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 2094 AN: 18076

East Asian (EAS) AF: 0.101 AC: 3023 AN: 29868

South Asian (SAS) AF: 0.117 AC: 6011 AN: 51450

European-Finnish (FIN) AF: 0.112 AC: 3722 AN: 33214

Middle Eastern (MID) AF: 0.105 AC: 430 AN: 4098

European-Non Finnish (NFE) AF: 0.0905 AC: 82141 AN: 907706

Other (OTH) AF: 0.105 AC: 4890 AN: 46492

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.00136 AC: 143 AN: 105204 Hom.: 0 Cov.: 22 AF XY: 0.00153 AC XY: 76 AN XY: 49646

African (AFR) AF: 0.00349 AC: 104 AN: 29808

American (AMR) AF: 0.000840 AC: 8 AN: 9524

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2654

East Asian (EAS) AF: 0.00 AC: 0 AN: 2666

South Asian (SAS) AF: 0.00137 AC: 4 AN: 2916

European-Finnish (FIN) AF: 0.00266 AC: 12 AN: 4506

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 168

European-Non Finnish (NFE) AF: 0.000236 AC: 12 AN: 50838

Other (OTH) AF: 0.00215 AC: 3 AN: 1394

Alfa AF: 0.00 Hom.: 62

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	TARS1-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.69
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs35931457; hg19: chr5-33453368; COSMIC: COSV105019566; COSMIC: COSV105019566;