TOR3A p.Phe13Leu

Variant names:

• chr1-179082167-C-A
• NM_022371.4:c.39C>A
• TOR3A p.Phe13Leu

Your query was ambiguous. Multiple possible variants found:

• chr1-179082167-C-A
• chr1-179082167-C-G
• chr1-179082165-T-C
• chr1-179082165-TTC-CTT
• chr1-179082165-TTC-CTA
• chr1-179082165-TTC-CTG

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_022371.4(TOR3A):​c.39C>A​(p.Phe13Leu) 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: 34)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TOR3A NM_022371.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825
• Publications: 0 publications found

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]

ENSG00000308086 (HGNC:):

ACMG classification

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=0.030139297).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022371.4. 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
	TOR3A	NM_022371.4	MANE Select	c.39C>A	p.Phe13Leu	missense	Exon 1 of 6	NP_071766.2	Q9H497-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TOR3A	ENST00000367627.8	TSL:1 MANE Select	c.39C>A	p.Phe13Leu	missense	Exon 1 of 6	ENSP00000356599.3	Q9H497-1
	TOR3A	ENST00000352445.10	TSL:1	c.39C>A	p.Phe13Leu	missense	Exon 1 of 6	ENSP00000335351.6	Q9H497-2
	TOR3A	ENST00000943766.1		c.39C>A	p.Phe13Leu	missense	Exon 1 of 6	ENSP00000613825.1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD2 exomes AF: 0.00 AC: 0 AN: 104902 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1354538 Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0 AN XY: 669236

African (AFR) AF: 0.00 AC: 0 AN: 27522

American (AMR) AF: 0.00 AC: 0 AN: 32354

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23104

East Asian (EAS) AF: 0.00 AC: 0 AN: 32190

South Asian (SAS) AF: 0.00 AC: 0 AN: 75922

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 34136

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4170

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1068790

Other (OTH) AF: 0.00 AC: 0 AN: 56350

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	0.34
DANN	Benign	0.62
DEOGEN2	Benign	0.016	T
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.5
FATHMM_MKL	Benign	0.14	N
LIST_S2	Benign	0.21	T
M_CAP	Benign	0.0036	T
MetaRNN	Benign	0.030	T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	-0.60	N
PhyloP100		-0.82
PrimateAI	Uncertain	0.70	T
PROVEAN	Benign	1.4	N
REVEL	Benign	0.074
Sift	Benign	1.0	T
Sift4G	Benign	1.0	T
PromoterAI		-0.073	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.8
Varity_R		0.11
gMVP		0.18
Mutation Taster		=99/1	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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr1-179051302;