rs10514164

chr5-79668906-T-G

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Moderate BP7 BA1

The NM_001114394.3(TENT2):c.1086T>G(p.Pro362=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0196 in 1,612,488 control chromosomes in the GnomAD database, including 1,585 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.028 (218 hom., cov: 31)
  • Exomes 𝑓: 0.019 (1367 hom.)
• Consequence: TENT2 NM_001114394.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.40

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 Benign. Variant got -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BP7: Synonymous conserved (PhyloP=3.4 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENT2	NM_001114394.3	c.1086T>G	p.Pro362=	synonymous_variant	12/15	ENST00000453514.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENT2	ENST00000453514.6	c.1086T>G	p.Pro362=	synonymous_variant	12/15	5	NM_001114394.3	A1

Frequencies

GnomAD3 genomes AF: 0.0278 AC: 4223 AN: 152178 Hom.: 218 Cov.: 31

Gnomad AFR AF: 0.0254

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.0252

Gnomad SAS AF: 0.0466

Gnomad FIN AF: 0.00668

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00876

Gnomad OTH AF: 0.0320

GnomAD3 exomes AF: 0.0449 AC: 11266 AN: 250882 Hom.: 1065 AF XY: 0.0384 AC XY: 5204 AN XY: 135646

Gnomad AFR exome AF: 0.0265

Gnomad AMR exome AF: 0.224

Gnomad ASJ exome AF: 0.00109

Gnomad EAS exome AF: 0.0276

Gnomad SAS exome AF: 0.0400

Gnomad FIN exome AF: 0.00814

Gnomad NFE exome AF: 0.00862

Gnomad OTH exome AF: 0.0365

GnomAD4 exome AF: 0.0187 AC: 27307 AN: 1460192 Hom.: 1367 Cov.: 31 AF XY: 0.0184 AC XY: 13375 AN XY: 726392

Gnomad4 AFR exome AF: 0.0261

Gnomad4 AMR exome AF: 0.212

Gnomad4 ASJ exome AF: 0.00184

Gnomad4 EAS exome AF: 0.0207

Gnomad4 SAS exome AF: 0.0400

Gnomad4 FIN exome AF: 0.00869

Gnomad4 NFE exome AF: 0.00986

Gnomad4 OTH exome AF: 0.0198

GnomAD4 genome AF: 0.0278 AC: 4237 AN: 152296 Hom.: 218 Cov.: 31 AF XY: 0.0306 AC XY: 2280 AN XY: 74480

Gnomad4 AFR AF: 0.0256

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.0250

Gnomad4 SAS AF: 0.0464

Gnomad4 FIN AF: 0.00668

Gnomad4 NFE AF: 0.00877

Gnomad4 OTH AF: 0.0317

Alfa AF: 0.0159 Hom.: 128

Bravo AF: 0.0390

Asia WGS AF: 0.0430 AC: 149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
Cadd	Benign	9.1
Dann	Benign	0.76

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

LitVar

Other links and lift over

dbSNP: rs10514164; hg19: chr5-78964729;