chr5-79668906-T-G

Variant names:

• chr5-79668906-T-G
• rs10514164
• NM_001114394.3:c.1086T>G

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_Moderate BP7 BA1

The NM_001114394.3(TENT2):​c.1086T>G​(p.Pro362Pro) 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. Synonymous variant affecting the same amino acid position (i.e. P362P) has been classified as Uncertain significance.

• 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
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001114394.3. 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
	TENT2	NM_001114394.3	MANE Select	c.1086T>G	p.Pro362Pro	synonymous	Exon 12 of 15	NP_001107866.1	Q6PIY7-1
	TENT2	NM_001349549.2		c.1161T>G	p.Pro387Pro	synonymous	Exon 12 of 15	NP_001336478.1
	TENT2	NM_001349550.2		c.1161T>G	p.Pro387Pro	synonymous	Exon 14 of 17	NP_001336479.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TENT2	ENST00000453514.6	TSL:5 MANE Select	c.1086T>G	p.Pro362Pro	synonymous	Exon 12 of 15	ENSP00000397563.1	Q6PIY7-1
	TENT2	ENST00000423041.6	TSL:1	c.1074T>G	p.Pro358Pro	synonymous	Exon 13 of 16	ENSP00000393412.2	Q6PIY7-2
	TENT2	ENST00000504233.5	TSL:1	c.957T>G	p.Pro319Pro	synonymous	Exon 11 of 14	ENSP00000421966.1	D6RAF2

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

GnomAD2 exomes AF: 0.0449 AC: 11266 AN: 250882 AF XY: 0.0384

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 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

African (AFR) AF: 0.0261 AC: 874 AN: 33440

American (AMR) AF: 0.212 AC: 9467 AN: 44642

Ashkenazi Jewish (ASJ) AF: 0.00184 AC: 48 AN: 26072

East Asian (EAS) AF: 0.0207 AC: 822 AN: 39636

South Asian (SAS) AF: 0.0400 AC: 3438 AN: 85980

European-Finnish (FIN) AF: 0.00869 AC: 463 AN: 53302

Middle Eastern (MID) AF: 0.00816 AC: 47 AN: 5762

European-Non Finnish (NFE) AF: 0.00986 AC: 10952 AN: 1111056

Other (OTH) AF: 0.0198 AC: 1196 AN: 60302

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

African (AFR) AF: 0.0256 AC: 1063 AN: 41576

American (AMR) AF: 0.136 AC: 2073 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00317 AC: 11 AN: 3472

East Asian (EAS) AF: 0.0250 AC: 130 AN: 5196

South Asian (SAS) AF: 0.0464 AC: 224 AN: 4826

European-Finnish (FIN) AF: 0.00668 AC: 71 AN: 10624

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00877 AC: 596 AN: 67990

Other (OTH) AF: 0.0317 AC: 67 AN: 2116

Alfa AF: 0.0166 Hom.: 271

Bravo AF: 0.0390

Asia WGS AF: 0.0430 AC: 149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	9.1
DANN	Benign	0.76
PhyloP100		3.4
Mutation Taster		=100/0	polymorphism (auto)

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: rs10514164; hg19: chr5-78964729;