6-81752010-ACCGCCGAAGTCGCCGCCGCCGAAGTCGCCGCCGCCGAAGTCGCCG-ACCGCCGAAGTCGCCGCCGCCGAAGTCGCCGCCGCCGAAGTCGCCGCCGCCGAAGTCGCCGCCGCCGAAGTCGCCGCCGCCGAAGTCGCCGCCGCCGAAGTCGCCGCCGCCGAAGTCGCCG
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM4
The NM_017633.3(TENT5A):c.131_132insCGGCGACTTCGGCGGCGGCGACTTCGGCGGCGGCGACTTCGGCGGCGGCGACTTCGGCGGCGGCGACTTCGGCGG(p.Gly44_Gly45insGlyAspPheGlyGlyGlyAspPheGlyGlyGlyAspPheGlyGlyGlyAspPheGlyGlyGlyAspPheGlyGly) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. G44G) has been classified as Benign.
Frequency
Genomes: 𝑓 0.0000072 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000012 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
TENT5A
NM_017633.3 disruptive_inframe_insertion
NM_017633.3 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0420
Publications
6 publications found
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 Gene-Disease associations (from GenCC):
- osteogenesis imperfecta, type 18Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- osteogenesis imperfectaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_017633.3.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_017633.3. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TENT5A | MANE Select | c.131_132insCGGCGACTTCGGCGGCGGCGACTTCGGCGGCGGCGACTTCGGCGGCGGCGACTTCGGCGGCGGCGACTTCGGCGG | p.Gly44_Gly45insGlyAspPheGlyGlyGlyAspPheGlyGlyGlyAspPheGlyGlyGlyAspPheGlyGlyGlyAspPheGlyGly | disruptive_inframe_insertion | Exon 2 of 3 | NP_060103.2 | Q96IP4-1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TENT5A | TSL:1 MANE Select | c.131_132insCGGCGACTTCGGCGGCGGCGACTTCGGCGGCGGCGACTTCGGCGGCGGCGACTTCGGCGGCGGCGACTTCGGCGG | p.Gly44_Gly45insGlyAspPheGlyGlyGlyAspPheGlyGlyGlyAspPheGlyGlyGlyAspPheGlyGlyGlyAspPheGlyGly | disruptive_inframe_insertion | Exon 2 of 3 | ENSP00000318298.6 | Q96IP4-1 | ||
| TENT5A | TSL:1 | c.374_375insCGGCGACTTCGGCGGCGGCGACTTCGGCGGCGGCGACTTCGGCGGCGGCGACTTCGGCGGCGGCGACTTCGGCGG | p.Gly125_Gly126insGlyAspPheGlyGlyGlyAspPheGlyGlyGlyAspPheGlyGlyGlyAspPheGlyGlyGlyAspPheGlyGly | disruptive_inframe_insertion | Exon 2 of 3 | ENSP00000358771.3 | Q5TF85 | ||
| TENT5A | TSL:1 | c.188_189insCGGCGACTTCGGCGGCGGCGACTTCGGCGGCGGCGACTTCGGCGGCGGCGACTTCGGCGGCGGCGACTTCGGCGG | p.Gly63_Gly64insGlyAspPheGlyGlyGlyAspPheGlyGlyGlyAspPheGlyGlyGlyAspPheGlyGlyGlyAspPheGlyGly | disruptive_inframe_insertion | Exon 2 of 3 | ENSP00000358769.3 | Q96IP4-2 |
Frequencies
GnomAD3 genomes 0.00000716 AC: 1AN: 139636Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
139636
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000116 AC: 14AN: 1201954Hom.: 0 Cov.: 34 AF XY: 0.0000116 AC XY: 7AN XY: 603570 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
14
AN:
1201954
Hom.:
Cov.:
34
AF XY:
AC XY:
7
AN XY:
603570
show subpopulations
African (AFR)
AF:
AC:
0
AN:
25452
American (AMR)
AF:
AC:
0
AN:
37204
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
22938
East Asian (EAS)
AF:
AC:
0
AN:
37832
South Asian (SAS)
AF:
AC:
1
AN:
74464
European-Finnish (FIN)
AF:
AC:
0
AN:
42970
Middle Eastern (MID)
AF:
AC:
0
AN:
4102
European-Non Finnish (NFE)
AF:
AC:
12
AN:
905602
Other (OTH)
AF:
AC:
1
AN:
51390
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.454
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.00000716 AC: 1AN: 139636Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 67628 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
139636
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
67628
show subpopulations
African (AFR)
AF:
AC:
0
AN:
36516
American (AMR)
AF:
AC:
0
AN:
14254
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3342
East Asian (EAS)
AF:
AC:
0
AN:
4560
South Asian (SAS)
AF:
AC:
0
AN:
4180
European-Finnish (FIN)
AF:
AC:
0
AN:
9518
Middle Eastern (MID)
AF:
AC:
0
AN:
288
European-Non Finnish (NFE)
AF:
AC:
1
AN:
64178
Other (OTH)
AF:
AC:
0
AN:
1922
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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