rs116567033

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_006567.5(FARS2):c.737C>T(p.Thr246Met) variant causes a missense change. The variant allele was found at a frequency of 0.00662 in 1,606,620 control chromosomes in the GnomAD database, including 55 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0045 ( 5 hom., cov: 32)

Exomes 𝑓: 0.0068 ( 50 hom. )

Consequence

FARS2
NM_006567.5 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts U:1B:7

Conservation

PhyloP100: 3.70

Variant links:

Genes affected

FARS2 (HGNC:21062): (phenylalanyl-tRNA synthetase 2, mitochondrial) This gene encodes a protein that transfers phenylalanine to its cognate tRNA. This protein localizes to the mitochondrion and plays a role in mitochondrial protein translation. Mutations in this gene can cause combined oxidative phosphorylation deficiency 14 (Alpers encephalopathy). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

FARS2 links:

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 (MetaRNN=0.0118563175).

BP6

Variant 6-5404666-C-T is Benign according to our data. Variant chr6-5404666-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 137291.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-5404666-C-T is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00446 (678/152064) while in subpopulation NFE AF= 0.00722 (491/68028). AF 95% confidence interval is 0.00669. There are 5 homozygotes in gnomad4. There are 308 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FARS2	NM_006567.5 link	c.737C>T	p.Thr246Met	missense_variant	Exon 3 of 7	ENST00000274680.9	NP_006558.1	O95363

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
FARS2	ENST00000274680.9 link	c.737C>T	p.Thr246Met	missense_variant	Exon 3 of 7	1	NM_006567.5	ENSP00000274680.4	O95363
FARS2	ENST00000324331.10 link	c.737C>T	p.Thr246Met	missense_variant	Exon 3 of 7	1		ENSP00000316335.5	O95363
FARS2	ENST00000445533.1 link	c.125C>T	p.Thr42Met	missense_variant	Exon 1 of 3	3		ENSP00000392525.1	Q5JRF7
FARS2	ENST00000648580.1 link	n.737C>T		non_coding_transcript_exon_variant	Exon 3 of 9			ENSP00000497889.1	A0A3B3ITR6

Frequencies

GnomAD3 genomes

AF:

0.00446

AC:

678

AN:

151974

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00109

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.00687

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00311

Gnomad FIN

AF:

0.00114

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00722

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00413

AC:

1027

AN:

248768

Hom.:

AF XY:

0.00417

AC XY:

560

AN XY:

134440

show subpopulations

Gnomad AFR exome

AF:

0.00142

Gnomad AMR exome

AF:

0.00257

Gnomad ASJ exome

AF:

0.000797

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00340

Gnomad FIN exome

AF:

0.000693

Gnomad NFE exome

AF:

0.00682

Gnomad OTH exome

AF:

0.00348

GnomAD4 exome

AF:

0.00685

AC:

9960

AN:

1454556

Hom.:

Cov.:

AF XY:

0.00676

AC XY:

4893

AN XY:

723332

show subpopulations

Gnomad4 AFR exome

AF:

0.00135

Gnomad4 AMR exome

AF:

0.00269

Gnomad4 ASJ exome

AF:

0.000539

Gnomad4 EAS exome

AF:

0.0000253

Gnomad4 SAS exome

AF:

0.00360

Gnomad4 FIN exome

AF:

0.00109

Gnomad4 NFE exome

AF:

0.00815

Gnomad4 OTH exome

AF:

0.00617

GnomAD4 genome

AF:

0.00446

AC:

678

AN:

152064

Hom.:

Cov.:

AF XY:

0.00414

AC XY:

308

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.00109

Gnomad4 AMR

AF:

0.00687

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00332

Gnomad4 FIN

AF:

0.00114

Gnomad4 NFE

AF:

0.00722

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00607

Hom.:

Bravo

AF:

0.00493

TwinsUK

AF:

0.00809

AC:

ALSPAC

AF:

0.00960

AC:

ESP6500AA

AF:

0.00227

AC:

ESP6500EA

AF:

0.00605

AC:

ExAC

AF:

0.00413

AC:

502

Asia WGS

AF:

0.000866

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Uncertain:1Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Uncertain:1Benign:3

Mar 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

FARS2: BP4, BS2 -

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Nov 12, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 23, 2016

Mayo Clinic Laboratories, Mayo Clinic

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Combined oxidative phosphorylation defect type 14

Benign:3

May 28, 2019

Mendelics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 13, 2018

Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 30, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

Apr 02, 2014

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.097

BayesDel_addAF

Benign

-0.32

BayesDel_noAF

Benign

-0.23

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.30

T;T;T

Eigen

Uncertain

0.32

Eigen_PC

Benign

0.17

FATHMM_MKL

Benign

0.68

LIST_S2

Pathogenic

0.98

.;D;D

M_CAP

Benign

0.024

MetaRNN

Benign

0.012

T;T;T

MetaSVM

Benign

-0.76

MutationAssessor

Uncertain

2.8

M;M;.

PrimateAI

Benign

0.47

PROVEAN

Uncertain

-3.5

D;D;D

REVEL

Uncertain

0.32

Sift

Uncertain

0.027

D;D;T

Sift4G

Benign

0.073

T;T;D

Polyphen

1.0

D;D;.

Vest4

0.61

MVP

0.82

MPC

0.66

ClinPred

0.017

GERP RS

4.4

Varity_R

0.26

gMVP

0.73

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over