10-73130845-C-T
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015901.6(NUDT13):c.1001C>T(p.Ser334Phe) variant causes a missense change. The variant allele was found at a frequency of 0.000658 in 1,613,952 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 (★).
Frequency
Genomes: 𝑓 0.00079 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00064 ( 0 hom. )
Consequence
NUDT13
NM_015901.6 missense
NM_015901.6 missense
Scores
4
5
8
Clinical Significance
Conservation
PhyloP100: 6.95
Genes affected
NUDT13 (HGNC:18827): (nudix hydrolase 13) Predicted to enable NADH pyrophosphatase activity. Predicted to be involved in NADH metabolic process and NADP catabolic process. Predicted to be located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]
ECD (HGNC:17029): (ecdysoneless cell cycle regulator) Enables histone acetyltransferase binding activity. Involved in positive regulation of transcription by RNA polymerase II. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.037146777).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUDT13 | NM_015901.6 | c.1001C>T | p.Ser334Phe | missense_variant | 9/9 | ENST00000357321.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUDT13 | ENST00000357321.9 | c.1001C>T | p.Ser334Phe | missense_variant | 9/9 | 5 | NM_015901.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000796 AC: 121AN: 152104Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000581 AC: 146AN: 251402Hom.: 0 AF XY: 0.000626 AC XY: 85AN XY: 135882
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GnomAD4 exome AF: 0.000644 AC: 941AN: 1461730Hom.: 0 Cov.: 31 AF XY: 0.000641 AC XY: 466AN XY: 727188
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GnomAD4 genome AF: 0.000795 AC: 121AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.000766 AC XY: 57AN XY: 74432
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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 | Sep 15, 2021 | The c.1001C>T (p.S334F) alteration is located in exon 9 (coding exon 8) of the NUDT13 gene. This alteration results from a C to T substitution at nucleotide position 1001, causing the serine (S) at amino acid position 334 to be replaced by a phenylalanine (F). 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
Uncertain
DANN
Uncertain
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D;N
REVEL
Uncertain
Sift
Pathogenic
D;D;D;D
Sift4G
Pathogenic
D;D;D;D
Polyphen
0.83, 0.090
.;.;P;B
Vest4
MVP
MPC
0.10
ClinPred
T
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