Genetic Variant TOR3A:p.Phe13Val (chr1-179082165-T-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_022371.4(TOR3A):c.37T>G(p.Phe13Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 37)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

TOR3A
NM_022371.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.48

Publications

31 publications found

Variant links:

Genes affected

TOR3A (HGNC:11997): (torsin family 3 member A) Predicted to enable ATP binding activity. Located in endoplasmic reticulum lumen. [provided by Alliance of Genome Resources, Apr 2022]

TOR3A links:

ENSG00000308086 (HGNC:):

ENSG00000308086 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.042000145).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TOR3A	NM_022371.4 link	c.37T>G	p.Phe13Val	missense_variant	Exon 1 of 6	ENST00000367627.8	NP_071766.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TOR3A	ENST00000367627.8 link	c.37T>G	p.Phe13Val	missense_variant	Exon 1 of 6	1	NM_022371.4	ENSP00000356599.3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1355330

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

669720

African (AFR)

AF:

0.00

AC:

AN:

27540

American (AMR)

AF:

0.00

AC:

AN:

32320

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

23028

East Asian (EAS)

AF:

0.00

AC:

AN:

32112

South Asian (SAS)

AF:

0.00

AC:

AN:

75878

European-Finnish (FIN)

AF:

0.00

AC:

AN:

34074

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4146

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1069872

Other (OTH)

AF:

0.00

AC:

AN:

56360

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

55812

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.076

BayesDel_addAF

Benign

-0.23

BayesDel_noAF

Benign

-0.57

CADD

Benign

4.0

(source)

DANN

Benign

0.34

DEOGEN2

Benign

0.021

T;T;.

Eigen

Benign

-1.9

Eigen_PC

Benign

-2.0

FATHMM_MKL

Benign

0.090

LIST_S2

Benign

0.22

T;T;T

M_CAP

Benign

0.0022

MetaRNN

Benign

0.042

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.0

N;.;N

PhyloP100

-1.5

PrimateAI

Uncertain

0.69

PROVEAN

Benign

0.36

N;N;N

REVEL

Benign

0.033

Sift

Benign

0.20

T;T;T

Sift4G

Benign

0.38

T;T;T

Vest4

0.063

ClinPred

0.10

GERP RS

-0.79

PromoterAI

0.062

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

Varity_R

0.055

gMVP

0.32

Mutation Taster

=99/1

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over