Variant chr6-81752010-ACCGCCGAAGTCGCCG-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM4BP6_Very_StrongBA1

The NM_017633.3(TENT5A):c.117_131delCGGCGACTTCGGCGG(p.Gly40_Gly44del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.2 in 1,340,024 control chromosomes in the GnomAD database, including 44,155 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.23 ( 3795 hom., cov: 0)

Exomes 𝑓: 0.20 ( 40360 hom. )

Consequence

TENT5A
NM_017633.3 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 5.41

Variant links:

Genes affected

TENT5A (HGNC:18345): (terminal nucleotidyltransferase 5A) Enables RNA binding activity. Predicted to be involved in mRNA stabilization. Predicted to act upstream of or within response to bacterium. Implicated in lung non-small cell carcinoma; osteoarthritis; and osteogenesis imperfecta type 18. [provided by Alliance of Genome Resources, Apr 2022]

TENT5A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_017633.3.

BP6

Variant 6-81752010-ACCGCCGAAGTCGCCG-A is Benign according to our data. Variant chr6-81752010-ACCGCCGAAGTCGCCG-A is described in ClinVar as [Benign]. Clinvar id is 402846.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-81752010-ACCGCCGAAGTCGCCG-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TENT5A	NM_017633.3 linkuse as main transcript	c.117_131delCGGCGACTTCGGCGG	p.Gly40_Gly44del	disruptive_inframe_deletion	2/3	ENST00000320172.11	NP_060103.2	Q96IP4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TENT5A	ENST00000320172.11 linkuse as main transcript	c.117_131delCGGCGACTTCGGCGG	p.Gly40_Gly44del	disruptive_inframe_deletion	2/3	1	NM_017633.3	ENSP00000318298.6	Q96IP4-1
TENT5A	ENST00000369756.3 linkuse as main transcript	c.360_374delCGGCGACTTCGGCGG	p.Gly121_Gly125del	disruptive_inframe_deletion	2/3	1		ENSP00000358771.3	Q5TF85
TENT5A	ENST00000369754.7 linkuse as main transcript	c.174_188delCGGCGACTTCGGCGG	p.Gly59_Gly63del	disruptive_inframe_deletion	2/3	1		ENSP00000358769.3	Q96IP4-2

Frequencies

GnomAD3 genomes

AF:

0.231

AC:

32262

AN:

139508

Hom.:

3797

Cov.:

show subpopulations

Gnomad AFR

AF:

0.141

Gnomad AMI

AF:

0.319

Gnomad AMR

AF:

0.271

Gnomad ASJ

AF:

0.383

Gnomad EAS

AF:

0.149

Gnomad SAS

AF:

0.303

Gnomad FIN

AF:

0.307

Gnomad MID

AF:

0.271

Gnomad NFE

AF:

0.253

Gnomad OTH

AF:

0.263

GnomAD4 exome

AF:

0.197

AC:

235921

AN:

1200438

Hom.:

40360

AF XY:

0.198

AC XY:

119588

AN XY:

602938

show subpopulations

Gnomad4 AFR exome

AF:

0.119

Gnomad4 AMR exome

AF:

0.242

Gnomad4 ASJ exome

AF:

0.339

Gnomad4 EAS exome

AF:

0.121

Gnomad4 SAS exome

AF:

0.242

Gnomad4 FIN exome

AF:

0.259

Gnomad4 NFE exome

AF:

0.189

Gnomad4 OTH exome

AF:

0.204

GnomAD4 genome

AF:

0.231

AC:

32254

AN:

139586

Hom.:

3795

Cov.:

AF XY:

0.234

AC XY:

15839

AN XY:

67668

show subpopulations

Gnomad4 AFR

AF:

0.141

Gnomad4 AMR

AF:

0.271

Gnomad4 ASJ

AF:

0.383

Gnomad4 EAS

AF:

0.149

Gnomad4 SAS

AF:

0.302

Gnomad4 FIN

AF:

0.307

Gnomad4 NFE

AF:

0.253

Gnomad4 OTH

AF:

0.262

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 12, 2019	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over