5-6739764-A-C
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The ENST00000230859.8(TENT4A):āc.920A>Cā(p.Glu307Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000155 in 1,613,970 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ).
Frequency
Genomes: š 0.000092 ( 0 hom., cov: 33)
Exomes š: 0.0000075 ( 0 hom. )
Consequence
TENT4A
ENST00000230859.8 missense
ENST00000230859.8 missense
Scores
1
5
8
Clinical Significance
Conservation
PhyloP100: 6.36
Genes affected
TENT4A (HGNC:16705): (terminal nucleotidyltransferase 4A) The protein encoded by this gene is a DNA polymerase that is likely involved in DNA repair. In addition, the encoded protein may be required for sister chromatid adhesion. Alternatively spliced transcript variants that encode different isoforms have been described. [provided by RefSeq, Jan 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.1551556).
BS2
High AC in GnomAd4 at 14 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TENT4A | NM_006999.6 | c.920A>C | p.Glu307Ala | missense_variant | 4/13 | ENST00000230859.8 | NP_008930.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TENT4A | ENST00000230859.8 | c.920A>C | p.Glu307Ala | missense_variant | 4/13 | 1 | NM_006999.6 | ENSP00000230859 | ||
TENT4A | ENST00000631941.2 | c.170A>C | p.Glu57Ala | missense_variant | 4/13 | 5 | ENSP00000488642 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152110Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251438Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135912
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GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461860Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727236
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GnomAD4 genome AF: 0.0000920 AC: 14AN: 152110Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74310
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 09, 2023 | The c.170A>C (p.E57A) alteration is located in exon 4 (coding exon 3) of the PAPD7 gene. This alteration results from a A to C substitution at nucleotide position 170, causing the glutamic acid (E) at amino acid position 57 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
D
PrimateAI
Pathogenic
D
REVEL
Benign
Sift4G
Uncertain
D;T
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at