rs151126262

Variant names:

• chr5-79641152-C-G
• NM_001114394.3:c.628C>G

Your query was ambiguous. Multiple possible variants found:

• chr5-79641152-C-G
• chr5-79641152-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001114394.3(TENT2):​c.628C>G​(p.Arg210Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000014 in 1,425,254 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: TENT2 NM_001114394.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.13

Genes affected

TENT2 (HGNC:26776): (terminal nucleotidyltransferase 2) Enables 5'-3' RNA polymerase activity and polynucleotide adenylyltransferase activity. Involved in RNA metabolic process and negative regulation of RNA catabolic process. Predicted to be located in nucleus. Predicted to be part of nuclear RNA-directed RNA polymerase complex. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TENT2	NM_001114394.3	c.628C>G	p.Arg210Gly	missense_variant	Exon 6 of 15	ENST00000453514.6	NP_001107866.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TENT2	ENST00000453514.6	c.628C>G	p.Arg210Gly	missense_variant	Exon 6 of 15	5	NM_001114394.3	ENSP00000397563.1
TENT2	ENST00000423041.6	c.628C>G	p.Arg210Gly	missense_variant	Exon 7 of 16	1		ENSP00000393412.2
TENT2	ENST00000504233.5	c.628C>G	p.Arg210Gly	missense_variant	Exon 6 of 14	1		ENSP00000421966.1
TENT2	ENST00000296783.7	c.628C>G	p.Arg210Gly	missense_variant	Exon 7 of 16	2		ENSP00000296783.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000140 AC: 2 AN: 1425254 Hom.: 0 Cov.: 30 AF XY: 0.00000282 AC XY: 2 AN XY: 708934

Gnomad4 AFR exome AF: 0.0000324

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.0000170

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.63
BayesDel_addAF	Pathogenic	0.22	D
BayesDel_noAF	Uncertain	0.080
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.25	T;.;T;T;T
Eigen	Uncertain	0.36
Eigen_PC	Uncertain	0.36
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Uncertain	0.94	D;D;D;.;.
M_CAP	Benign	0.039	D
MetaRNN	Uncertain	0.70	D;D;D;D;D
MetaSVM	Benign	-0.80	T
MutationAssessor	Uncertain	2.7	M;M;.;M;M
PrimateAI	Uncertain	0.69	T
PROVEAN	Benign	-1.8	N;N;N;N;N
REVEL	Uncertain	0.34
Sift	Benign	0.083	T;T;T;T;T
Sift4G	Benign	0.50	T;T;D;T;T
Polyphen		0.91	P;P;D;P;P
Vest4		0.81
MutPred		0.44		Loss of solvent accessibility (P = 0.0769);Loss of solvent accessibility (P = 0.0769);Loss of solvent accessibility (P = 0.0769);Loss of solvent accessibility (P = 0.0769);Loss of solvent accessibility (P = 0.0769);
MVP		0.53
MPC		0.92
ClinPred		0.92	D
GERP RS		3.9
Varity_R		0.35
gMVP		0.67

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-78936975;