X-80442870-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_152630.5(TENT5D):c.331T>C(p.Phe111Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00013 in 1,209,189 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 65 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000081 ( 0 hom., 4 hem., cov: 23)
Exomes 𝑓: 0.00013 ( 0 hom. 61 hem. )
Consequence
TENT5D
NM_152630.5 missense
NM_152630.5 missense
Scores
1
4
11
Clinical Significance
Conservation
PhyloP100: 3.76
Genes affected
TENT5D (HGNC:28399): (terminal nucleotidyltransferase 5D) Antibodies against the protein encoded by this gene were found only in plasma from cancer patients. While it may be a target for immunotherapy, the function of this gene is unknown. [provided by RefSeq, Dec 2009]
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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=0.16051328).
BS2
?
High Hemizygotes in GnomAd at 4 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TENT5D | NM_152630.5 | c.331T>C | p.Phe111Leu | missense_variant | 3/3 | ENST00000308293.6 | |
TENT5D | NM_001170574.2 | c.331T>C | p.Phe111Leu | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TENT5D | ENST00000308293.6 | c.331T>C | p.Phe111Leu | missense_variant | 3/3 | 1 | NM_152630.5 | P1 | |
TENT5D | ENST00000538312.5 | c.331T>C | p.Phe111Leu | missense_variant | 5/5 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000808 AC: 9AN: 111420Hom.: 0 Cov.: 23 AF XY: 0.000119 AC XY: 4AN XY: 33698
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.0000822 AC: 15AN: 182568Hom.: 0 AF XY: 0.000104 AC XY: 7AN XY: 67398
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GnomAD4 exome AF: 0.000135 AC: 148AN: 1097769Hom.: 0 Cov.: 31 AF XY: 0.000168 AC XY: 61AN XY: 363315
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GnomAD4 genome ? AF: 0.0000808 AC: 9AN: 111420Hom.: 0 Cov.: 23 AF XY: 0.000119 AC XY: 4AN XY: 33698
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2023 | The c.331T>C (p.F111L) alteration is located in exon 5 (coding exon 1) of the FAM46D gene. This alteration results from a T to C substitution at nucleotide position 331, causing the phenylalanine (F) at amino acid position 111 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;T
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;.
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MutPred
Loss of methylation at K114 (P = 0.0916);Loss of methylation at K114 (P = 0.0916);
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
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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