5-79647825-G-C

Variant names:

• chr5-79647825-G-C
• rs6859704
• NM_001114394.3:c.822-792G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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 -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TENT2	NM_001114394.3	MANE Select	c.822-792G>C		intron	N/A	NP_001107866.1
	TENT2	NM_001349549.2		c.897-792G>C		intron	N/A	NP_001336478.1
	TENT2	NM_001349550.2		c.897-792G>C		intron	N/A	NP_001336479.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TENT2	ENST00000453514.6	TSL:5 MANE Select	c.822-792G>C		intron	N/A	ENSP00000397563.1
	TENT2	ENST00000423041.6	TSL:1	c.810-792G>C		intron	N/A	ENSP00000393412.2
	TENT2	ENST00000504233.5	TSL:1	c.822-792G>C		intron	N/A	ENSP00000421966.1

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

African (AFR) AF: 0.419 AC: 17344 AN: 41362

American (AMR) AF: 0.236 AC: 3602 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 357 AN: 3460

East Asian (EAS) AF: 0.153 AC: 790 AN: 5176

South Asian (SAS) AF: 0.127 AC: 612 AN: 4816

European-Finnish (FIN) AF: 0.0987 AC: 1035 AN: 10490

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.104 AC: 7077 AN: 67946

Other (OTH) AF: 0.198 AC: 417 AN: 2106

Alfa AF: 0.0570 Hom.: 59

Bravo AF: 0.231

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.41
PhyloP100		-0.58
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: rs6859704; hg19: chr5-78943648; COSMIC: COSV57135752; COSMIC: COSV57135752;