chr1-220126693-T-C

Position:

• chr1-220126693-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_018060.4(IARS2):​c.1744-57T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0699 in 1,244,492 control chromosomes in the GnomAD database, including 3,420 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.054 (309 hom., cov: 32)
  • Exomes 𝑓: 0.072 (3111 hom.)
• Consequence: IARS2 NM_018060.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.160

Genes affected

IARS2 (HGNC:29685): (isoleucyl-tRNA synthetase 2, mitochondrial) 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. Two forms of isoleucine-tRNA synthetase exist, a cytoplasmic form and a mitochondrial form. This gene encodes the mitochondrial isoleucine-tRNA synthetase which belongs to the class-I aminoacyl-tRNA synthetase family. [provided by RefSeq, Dec 2014]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 1-220126693-T-C is Benign according to our data. Variant chr1-220126693-T-C is described in ClinVar as [Benign]. Clinvar id is 676218.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IARS2	NM_018060.4	c.1744-57T>C		intron_variant		ENST00000366922.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IARS2	ENST00000366922.3	c.1744-57T>C		intron_variant		1	NM_018060.4	P1
IARS2	ENST00000490891.1	n.128-57T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0537 AC: 8176 AN: 152138 Hom.: 307 Cov.: 32

Gnomad AFR AF: 0.0132

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.0458

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0418

Gnomad SAS AF: 0.0585

Gnomad FIN AF: 0.0662

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0754

Gnomad OTH AF: 0.0613

GnomAD4 exome AF: 0.0722 AC: 78847 AN: 1092236 Hom.: 3111 AF XY: 0.0725 AC XY: 40569 AN XY: 559914

Gnomad4 AFR exome AF: 0.0107

Gnomad4 AMR exome AF: 0.0367

Gnomad4 ASJ exome AF: 0.104

Gnomad4 EAS exome AF: 0.0428

Gnomad4 SAS exome AF: 0.0632

Gnomad4 FIN exome AF: 0.0676

Gnomad4 NFE exome AF: 0.0777

Gnomad4 OTH exome AF: 0.0702

GnomAD4 genome AF: 0.0537 AC: 8177 AN: 152256 Hom.: 309 Cov.: 32 AF XY: 0.0530 AC XY: 3942 AN XY: 74442

Gnomad4 AFR AF: 0.0131

Gnomad4 AMR AF: 0.0457

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.0417

Gnomad4 SAS AF: 0.0591

Gnomad4 FIN AF: 0.0662

Gnomad4 NFE AF: 0.0753

Gnomad4 OTH AF: 0.0611

Alfa AF: 0.0731 Hom.: 590

Bravo AF: 0.0499

Asia WGS AF: 0.0350 AC: 122 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2018	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.8
DANN	Benign	0.82
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Other links and lift over

dbSNP: rs2289191; hg19: chr1-220300035; COSMIC: COSV56963881;