chr6-81749628-CT-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_017633.3(TENT5A):c.*66del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 1,008,774 control chromosomes in the GnomAD database, including 592 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.066 ( 437 hom., cov: 30)
Exomes 𝑓: 0.19 ( 155 hom. )
Consequence
TENT5A
NM_017633.3 3_prime_UTR
NM_017633.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.316
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 6-81749628-CT-C is Benign according to our data. Variant chr6-81749628-CT-C is described in ClinVar as [Benign]. Clinvar id is 1282756.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TENT5A | NM_017633.3 | c.*66del | 3_prime_UTR_variant | 3/3 | ENST00000320172.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TENT5A | ENST00000320172.11 | c.*66del | 3_prime_UTR_variant | 3/3 | 1 | NM_017633.3 | A2 | ||
TENT5A | ENST00000369754.7 | c.*66del | 3_prime_UTR_variant | 3/3 | 1 | P4 | |||
TENT5A | ENST00000369756.3 | c.*66del | 3_prime_UTR_variant | 3/3 | 1 | ||||
TENT5A | ENST00000412306.1 | c.223+1961del | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0660 AC: 9209AN: 139590Hom.: 439 Cov.: 30
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GnomAD4 exome AF: 0.191 AC: 165862AN: 869206Hom.: 155 Cov.: 0 AF XY: 0.190 AC XY: 80983AN XY: 425324
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GnomAD4 genome ? AF: 0.0660 AC: 9211AN: 139568Hom.: 437 Cov.: 30 AF XY: 0.0631 AC XY: 4260AN XY: 67504
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 11, 2021 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at