chr5-79668176-G-A

Variant names:

• chr5-79668176-G-A
• rs6877794
• NM_001114394.3:c.1072-716G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001114394.3(TENT2):​c.1072-716G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,796 control chromosomes in the GnomAD database, including 17,758 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 0.44 (17758 hom., cov: 31)
• Consequence: TENT2 NM_001114394.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.973
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TENT2	NM_001114394.3	c.1072-716G>A		intron_variant	Intron 11 of 14	ENST00000453514.6	NP_001107866.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TENT2	ENST00000453514.6	c.1072-716G>A		intron_variant	Intron 11 of 14	5	NM_001114394.3	ENSP00000397563.1

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66523 AN: 151678 Hom.: 17705 Cov.: 31

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.439 AC: 66635 AN: 151796 Hom.: 17758 Cov.: 31 AF XY: 0.439 AC XY: 32585 AN XY: 74174

African (AFR) AF: 0.746 AC: 30914 AN: 41454

American (AMR) AF: 0.450 AC: 6855 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 843 AN: 3468

East Asian (EAS) AF: 0.524 AC: 2710 AN: 5170

South Asian (SAS) AF: 0.335 AC: 1612 AN: 4806

European-Finnish (FIN) AF: 0.319 AC: 3351 AN: 10492

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19113 AN: 67848

Other (OTH) AF: 0.402 AC: 849 AN: 2110

Alfa AF: 0.333 Hom.: 31105

Bravo AF: 0.466

Asia WGS AF: 0.493 AC: 1711 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.9
DANN	Benign	0.38
PhyloP100		0.97
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: rs6877794; hg19: chr5-78963999;