Variant rs2066411 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017709.4(TENT5C):c.*84A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 1,159,988 control chromosomes in the GnomAD database, including 31,647 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 0.24 ( 4086 hom., cov: 29)

Exomes 𝑓: 0.23 ( 27561 hom. )

Consequence

TENT5C
NM_017709.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.16

Variant links:

Genes affected

TENT5C (HGNC:24712): (terminal nucleotidyltransferase 5C) Enables RNA adenylyltransferase activity. Involved in mRNA stabilization. Located in cytoplasm and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

TENT5C links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TENT5C	NM_017709.4 linkuse as main transcript	c.*84A>G		3_prime_UTR_variant	2/2	ENST00000369448.4	NP_060179.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TENT5C	ENST00000369448.4 linkuse as main transcript	c.*84A>G		3_prime_UTR_variant	2/2	1	NM_017709.4	ENSP00000358458	P1

Frequencies

GnomAD3 genomes

AF:

0.237

AC:

34981

AN:

147724

Hom.:

4083

Cov.:

show subpopulations

Gnomad AFR

AF:

0.205

Gnomad AMI

AF:

0.249

Gnomad AMR

AF:

0.320

Gnomad ASJ

AF:

0.306

Gnomad EAS

AF:

0.223

Gnomad SAS

AF:

0.281

Gnomad FIN

AF:

0.243

Gnomad MID

AF:

0.292

Gnomad NFE

AF:

0.229

Gnomad OTH

AF:

0.268

GnomAD4 exome

AF:

0.230

AC:

233007

AN:

1012222

Hom.:

27561

Cov.:

AF XY:

0.233

AC XY:

116822

AN XY:

501054

show subpopulations

Gnomad4 AFR exome

AF:

0.196

Gnomad4 AMR exome

AF:

0.321

Gnomad4 ASJ exome

AF:

0.299

Gnomad4 EAS exome

AF:

0.206

Gnomad4 SAS exome

AF:

0.308

Gnomad4 FIN exome

AF:

0.220

Gnomad4 NFE exome

AF:

0.222

Gnomad4 OTH exome

AF:

0.246

GnomAD4 genome

AF:

0.237

AC:

34992

AN:

147766

Hom.:

4086

Cov.:

AF XY:

0.244

AC XY:

17486

AN XY:

71712

show subpopulations

Gnomad4 AFR

AF:

0.205

Gnomad4 AMR

AF:

0.320

Gnomad4 ASJ

AF:

0.306

Gnomad4 EAS

AF:

0.223

Gnomad4 SAS

AF:

0.281

Gnomad4 FIN

AF:

0.243

Gnomad4 NFE

AF:

0.229

Gnomad4 OTH

AF:

0.267

Alfa

AF:

0.226

Hom.:

4581

Bravo

AF:

0.236

Asia WGS

AF:

0.247

AC:

856

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

DANN

Benign

0.87

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over