NM_001321783.2:c.1495T>C

Variant names:

• chr10-5739665-T-C
• rs2254067
• NM_001321783.2:c.1495T>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001321783.2(TASOR2):​c.1495T>C​(p.Cys499Arg) 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. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C499S) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 30)
• Consequence: TASOR2 NM_001321783.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.379
• Publications: 33 publications found

Genes affected

TASOR2 (HGNC:23484): (transcription activation suppressor family member 2) Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000226647 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08210695).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001321783.2. 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
	TASOR2	NM_001321783.2	MANE Select	c.1495T>C	p.Cys499Arg	missense	Exon 14 of 22	NP_001308712.2
	TASOR2	NM_001387328.1		c.2140T>C	p.Cys714Arg	missense	Exon 16 of 24	NP_001374257.1
	TASOR2	NM_001321784.2		c.1495T>C	p.Cys499Arg	missense	Exon 14 of 22	NP_001308713.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TASOR2	ENST00000695737.1	MANE Select	c.1495T>C	p.Cys499Arg	missense	Exon 14 of 22	ENSP00000512130.1
	TASOR2	ENST00000328090.9	TSL:1	c.1495T>C	p.Cys499Arg	missense	Exon 13 of 21	ENSP00000328426.5
	TASOR2	ENST00000699051.1		c.2278T>C	p.Cys760Arg	missense	Exon 17 of 25	ENSP00000514102.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 47

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Uncertain	0.013	T
BayesDel_noAF	Benign	-0.22
CADD	Benign	15
DANN	Benign	0.71
DEOGEN2	Benign	0.0042	T
Eigen	Benign	-0.97
Eigen_PC	Benign	-1.0
FATHMM_MKL	Benign	0.058	N
LIST_S2	Benign	0.44	T
M_CAP	Benign	0.024	T
MetaRNN	Benign	0.082	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.69	N
PhyloP100		0.38
PrimateAI	Benign	0.32	T
PROVEAN	Benign	0.050	N
REVEL	Benign	0.18
Sift	Uncertain	0.0020	D
Sift4G	Uncertain	0.039	D
Polyphen		0.010	B
Vest4		0.086
MutPred		0.16		Gain of solvent accessibility (P = 0.0246)
MVP		0.068
MPC		0.071
ClinPred		0.055	T
GERP RS		2.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.32
gMVP		0.13
Mutation Taster		=98/2	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: rs2254067; hg19: chr10-5781628;