Variant chr6-81752010-A-ACCGCCGAAGTCGCCGCCGCCGAAGTCGCCG 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.102_131dupCGGCGACTTCGGCGGCGGCGACTTCGGCGG(p.Gly44_Gly45insGlyAspPheGlyGlyGlyAspPheGlyGly) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0267 in 1,200,868 control chromosomes in the GnomAD database, including 1,386 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.075 ( 754 hom., cov: 0)

Exomes 𝑓: 0.027 ( 1386 hom. )

Failed GnomAD Quality Control

Consequence

TENT5A
NM_017633.3 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0420

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-A-ACCGCCGAAGTCGCCGCCGCCGAAGTCGCCG is Benign according to our data. Variant chr6-81752010-A-ACCGCCGAAGTCGCCGCCGCCGAAGTCGCCG is described in ClinVar as [Likely_benign]. Clinvar id is 1250446.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0572 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.102_131dupCGGCGACTTCGGCGGCGGCGACTTCGGCGG	p.Gly44_Gly45insGlyAspPheGlyGlyGlyAspPheGlyGly	disruptive_inframe_insertion	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.102_131dupCGGCGACTTCGGCGGCGGCGACTTCGGCGG	p.Gly44_Gly45insGlyAspPheGlyGlyGlyAspPheGlyGly	disruptive_inframe_insertion	2/3	1	NM_017633.3	ENSP00000318298.6	Q96IP4-1
TENT5A	ENST00000369756.3 linkuse as main transcript	c.345_374dupCGGCGACTTCGGCGGCGGCGACTTCGGCGG	p.Gly125_Gly126insGlyAspPheGlyGlyGlyAspPheGlyGly	disruptive_inframe_insertion	2/3	1		ENSP00000358771.3	Q5TF85
TENT5A	ENST00000369754.7 linkuse as main transcript	c.159_188dupCGGCGACTTCGGCGGCGGCGACTTCGGCGG	p.Gly63_Gly64insGlyAspPheGlyGlyGlyAspPheGlyGly	disruptive_inframe_insertion	2/3	1		ENSP00000358769.3	Q96IP4-2

Frequencies

GnomAD3 genomes

AF:

0.0748

AC:

10445

AN:

139558

Hom.:

755

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0997

Gnomad AMI

AF:

0.0535

Gnomad AMR

AF:

0.0851

Gnomad ASJ

AF:

0.0571

Gnomad EAS

AF:

0.0654

Gnomad SAS

AF:

0.0783

Gnomad FIN

AF:

0.0528

Gnomad MID

AF:

0.0764

Gnomad NFE

AF:

0.0637

Gnomad OTH

AF:

0.0625

GnomAD4 exome

AF:

0.0267

AC:

32116

AN:

1200868

Hom.:

1386

Cov.:

AF XY:

0.0283

AC XY:

17046

AN XY:

603070

show subpopulations

Gnomad4 AFR exome

AF:

0.0443

Gnomad4 AMR exome

AF:

0.0469

Gnomad4 ASJ exome

AF:

0.0367

Gnomad4 EAS exome

AF:

0.0485

Gnomad4 SAS exome

AF:

0.0586

Gnomad4 FIN exome

AF:

0.0548

Gnomad4 NFE exome

AF:

0.0197

Gnomad4 OTH exome

AF:

0.0370

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0748

AC:

10451

AN:

139636

Hom.:

754

Cov.:

AF XY:

0.0748

AC XY:

5061

AN XY:

67686

show subpopulations

Gnomad4 AFR

AF:

0.0999

Gnomad4 AMR

AF:

0.0849

Gnomad4 ASJ

AF:

0.0571

Gnomad4 EAS

AF:

0.0656

Gnomad4 SAS

AF:

0.0774

Gnomad4 FIN

AF:

0.0528

Gnomad4 NFE

AF:

0.0637

Gnomad4 OTH

AF:

0.0610

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 26, 2019	- -

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