chr5-79647825-G-C

Position:

• chr5-79647825-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001114394.3(TENT2):​c.822-792G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 151,800 control chromosomes in the GnomAD database, including 4,685 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 0.21 (4685 hom., cov: 32)
• Consequence: TENT2 NM_001114394.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TENT2	NM_001114394.3	c.822-792G>C		intron_variant		ENST00000453514.6	NP_001107866.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TENT2	ENST00000453514.6	c.822-792G>C		intron_variant		5	NM_001114394.3	ENSP00000397563	A1

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31402 AN: 151688 Hom.: 4671 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0987

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.198

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.207 AC: 31457 AN: 151800 Hom.: 4685 Cov.: 32 AF XY: 0.205 AC XY: 15221 AN XY: 74168

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.0987

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.198

Alfa AF: 0.0570 Hom.: 59

Bravo AF: 0.231

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.41

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: rs6859704; hg19: chr5-78943648; COSMIC: COSV57135752; COSMIC: COSV57135752;