chr1-179082165-T-G

Variant names:

• chr1-179082165-T-G
• rs2296377
• NM_022371.4:c.37T>G

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.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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 31 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=0.042000145).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TOR3A	NM_022371.4	MANE Select	c.37T>G	p.Phe13Val	missense	Exon 1 of 6	NP_071766.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TOR3A	ENST00000367627.8	TSL:1 MANE Select	c.37T>G	p.Phe13Val	missense	Exon 1 of 6	ENSP00000356599.3
	TOR3A	ENST00000352445.10	TSL:1	c.37T>G	p.Phe13Val	missense	Exon 1 of 6	ENSP00000335351.6
	TOR3A	ENST00000367625.8	TSL:3	c.37T>G	p.Phe13Val	missense	Exon 1 of 3	ENSP00000356597.4

Frequencies

GnomAD3 genomes Cov.: 37

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1355330 Hom.: 0 Cov.: 72 AF XY: 0.00 AC XY: 0 AN XY: 669720

African (AFR) AF: 0.00 AC: 0 AN: 27540

American (AMR) AF: 0.00 AC: 0 AN: 32320

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23028

East Asian (EAS) AF: 0.00 AC: 0 AN: 32112

South Asian (SAS) AF: 0.00 AC: 0 AN: 75878

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 34074

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4146

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1069872

Other (OTH) AF: 0.00 AC: 0 AN: 56360

GnomAD4 genome Cov.: 37

Alfa AF: 0.00 Hom.: 55812

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.076
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.57
CADD	Benign	4.0
DANN	Benign	0.34
DEOGEN2	Benign	0.021	T
Eigen	Benign	-1.9
Eigen_PC	Benign	-2.0
FATHMM_MKL	Benign	0.090	N
LIST_S2	Benign	0.22	T
M_CAP	Benign	0.0022	T
MetaRNN	Benign	0.042	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.0	N
PhyloP100		-1.5
PrimateAI	Uncertain	0.69	T
PROVEAN	Benign	0.36	N
REVEL	Benign	0.033
Sift	Benign	0.20	T
Sift4G	Benign	0.38	T
Polyphen		0.0030	B
Vest4		0.063
MutPred		0.27		Gain of MoRF binding (P = 0.073)
MVP		0.13
MPC		0.22
ClinPred		0.10	T
GERP RS		-0.79
PromoterAI		0.062	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
Varity_R		0.055
gMVP		0.32
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

Other links and lift over

dbSNP: rs2296377; hg19: chr1-179051300;