8-124504322-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_032026.4(TATDN1):c.542A>G(p.Glu181Gly) variant causes a missense change. The variant allele was found at a frequency of 0.0000864 in 1,607,876 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000091 ( 0 hom. )
Consequence
TATDN1
NM_032026.4 missense
NM_032026.4 missense
Scores
1
9
5
Clinical Significance
Conservation
PhyloP100: 6.22
Genes affected
TATDN1 (HGNC:24220): (TatD DNase domain containing 1) Predicted to enable 3'-5'-exodeoxyribonuclease activity. Predicted to be involved in DNA metabolic process and nucleic acid phosphodiester bond hydrolysis. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TATDN1 | NM_032026.4 | c.542A>G | p.Glu181Gly | missense_variant | 9/12 | ENST00000276692.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TATDN1 | ENST00000276692.11 | c.542A>G | p.Glu181Gly | missense_variant | 9/12 | 1 | NM_032026.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152164Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000844 AC: 21AN: 248754Hom.: 0 AF XY: 0.0000818 AC XY: 11AN XY: 134438
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GnomAD4 exome AF: 0.0000907 AC: 132AN: 1455712Hom.: 0 Cov.: 29 AF XY: 0.0000884 AC XY: 64AN XY: 723850
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GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74334
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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 | May 08, 2023 | The c.542A>G (p.E181G) alteration is located in exon 9 (coding exon 9) of the TATDN1 gene. This alteration results from a A to G substitution at nucleotide position 542, causing the glutamic acid (E) at amino acid position 181 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Pathogenic
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;T;.;.;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D;D;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D;D;D;D;D
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D;D
PrimateAI
Benign
T
Sift4G
Uncertain
D;T;D;D;D;D
Polyphen
0.051, 0.43
.;B;.;B;.;.
Vest4
MVP
MPC
0.041
ClinPred
D
GERP RS
Varity_R
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