rs6859704

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr5-79647825-G-A
• chr5-79647825-G-C

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_001114394.3(TENT2):​c.822-792G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00283 in 151,856 control chromosomes in the GnomAD database, including 2 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 0.0028 (2 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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS2: High Homozygotes in GnomAd4 at 2 AR gene

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>A		intron	N/A	NP_001107866.1
	TENT2	NM_001349549.2		c.897-792G>A		intron	N/A	NP_001336478.1
	TENT2	NM_001349550.2		c.897-792G>A		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>A		intron	N/A	ENSP00000397563.1
	TENT2	ENST00000423041.6	TSL:1	c.810-792G>A		intron	N/A	ENSP00000393412.2
	TENT2	ENST00000504233.5	TSL:1	c.822-792G>A		intron	N/A	ENSP00000421966.1

Frequencies

GnomAD3 genomes AF: 0.00283 AC: 430 AN: 151744 Hom.: 2 Cov.: 32

Gnomad AFR AF: 0.000872

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000985

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0141

Gnomad FIN AF: 0.00133

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.00360

Gnomad OTH AF: 0.00288

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

GnomAD4 genome AF: 0.00283 AC: 430 AN: 151856 Hom.: 2 Cov.: 32 AF XY: 0.00295 AC XY: 219 AN XY: 74206

African (AFR) AF: 0.000870 AC: 36 AN: 41390

American (AMR) AF: 0.000983 AC: 15 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0127 AC: 44 AN: 3460

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.0141 AC: 68 AN: 4818

European-Finnish (FIN) AF: 0.00133 AC: 14 AN: 10492

Middle Eastern (MID) AF: 0.00685 AC: 2 AN: 292

European-Non Finnish (NFE) AF: 0.00361 AC: 245 AN: 67954

Other (OTH) AF: 0.00285 AC: 6 AN: 2106

Alfa AF: 0.000335 Hom.: 59

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.90
PhyloP100		-0.58

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;