dbSNP rs1630312: TENT5C:p.His67Gln (chr1-117623069-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017709.4(TENT5C):c.201C>G(p.His67Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0682 in 1,614,004 control chromosomes in the GnomAD database, including 5,006 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: 𝑓 0.11 ( 1298 hom., cov: 32)

Exomes 𝑓: 0.064 ( 3708 hom. )

Consequence

TENT5C
NM_017709.4 missense

Scores

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: 0.434

Publications

27 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0017356277).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TENT5C	NM_017709.4 link	c.201C>G	p.His67Gln	missense_variant	Exon 2 of 2	ENST00000369448.4	NP_060179.2	Q5VWP2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TENT5C	ENST00000369448.4 link	c.201C>G	p.His67Gln	missense_variant	Exon 2 of 2	1	NM_017709.4	ENSP00000358458.3		Q5VWP2

Frequencies

GnomAD3 genomes

AF:

0.109

AC:

16591

AN:

152006

Hom.:

1297

Cov.:

show subpopulations

Gnomad AFR

AF:

0.219

Gnomad AMI

AF:

0.0956

Gnomad AMR

AF:

0.0821

Gnomad ASJ

AF:

0.0873

Gnomad EAS

AF:

0.110

Gnomad SAS

AF:

0.0634

Gnomad FIN

AF:

0.0676

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.0593

Gnomad OTH

AF:

0.116

GnomAD2 exomes

AF:

0.0774

AC:

19448

AN:

251420

AF XY:

0.0750

show subpopulations

Gnomad AFR exome

AF:

0.223

Gnomad AMR exome

AF:

0.0691

Gnomad ASJ exome

AF:

0.0841

Gnomad EAS exome

AF:

0.119

Gnomad FIN exome

AF:

0.0630

Gnomad NFE exome

AF:

0.0575

Gnomad OTH exome

AF:

0.0771

GnomAD4 exome

AF:

0.0639

AC:

93405

AN:

1461880

Hom.:

3708

Cov.:

AF XY:

0.0635

AC XY:

46170

AN XY:

727238

show subpopulations

African (AFR)

AF:

0.222

AC:

7432

AN:

33480

American (AMR)

AF:

0.0730

AC:

3263

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.0805

AC:

2103

AN:

26136

East Asian (EAS)

AF:

0.0884

AC:

3511

AN:

39700

South Asian (SAS)

AF:

0.0686

AC:

5916

AN:

86258

European-Finnish (FIN)

AF:

0.0616

AC:

3291

AN:

53420

Middle Eastern (MID)

AF:

0.109

AC:

631

AN:

5768

European-Non Finnish (NFE)

AF:

0.0561

AC:

62390

AN:

1112000

Other (OTH)

AF:

0.0806

AC:

4868

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

5756

11511

17267

23022

28778

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.109

AC:

16618

AN:

152124

Hom.:

1298

Cov.:

AF XY:

0.109

AC XY:

8118

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.219

AC:

9080

AN:

41468

American (AMR)

AF:

0.0819

AC:

1253

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0873

AC:

303

AN:

3472

East Asian (EAS)

AF:

0.110

AC:

569

AN:

5178

South Asian (SAS)

AF:

0.0633

AC:

305

AN:

4822

European-Finnish (FIN)

AF:

0.0676

AC:

715

AN:

10570

Middle Eastern (MID)

AF:

0.0918

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0593

AC:

4035

AN:

67996

Other (OTH)

AF:

0.115

AC:

244

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

718

1435

2153

2870

3588

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0146

Hom.:

2339

TwinsUK

AF:

0.0566

AC:

210

ALSPAC

AF:

0.0527

AC:

203

ExAC

AF:

0.0790

AC:

9598

EpiCase

AF:

0.0642

EpiControl

AF:

0.0663

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

LINK: link

Submissions by phenotype

not specified

Other:1

Sep 19, 2013

ITMI

Significance:not provided

Review Status:no classification provided

Collection Method:reference population

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.085

BayesDel_addAF

Benign

-0.76

BayesDel_noAF

Benign

-0.72

CADD

Benign

(source)

DANN

Benign

0.95

DEOGEN2

Benign

0.032

Eigen

Benign

-0.38

Eigen_PC

Benign

-0.16

FATHMM_MKL

Benign

0.32

LIST_S2

Benign

0.47

MetaRNN

Benign

0.0017

MetaSVM

Benign

-1.0

PhyloP100

0.43

PrimateAI

Benign

0.38

PROVEAN

Benign

-0.020

REVEL

Benign

0.087

Sift

Benign

0.18

Sift4G

Benign

0.12

Polyphen

0.0

Vest4

0.024

MutPred

0.14

Loss of methylation at R70 (P = 0.0447);

MPC

0.58

ClinPred

0.020

GERP RS

5.8

Varity_R

0.21

gMVP

0.18

Mutation Taster

=92/8

polymorphism (auto)

(source)

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

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rs1630312

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over