chr1-6625258-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001195753.2(THAP3):c.40T>C(p.Tyr14His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000142 in 1,544,744 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000086 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000065 ( 0 hom. )
Consequence
THAP3
NM_001195753.2 missense
NM_001195753.2 missense
Scores
6
9
4
Clinical Significance
Conservation
PhyloP100: 1.47
Genes affected
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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 |
---|---|---|---|---|---|---|---|
THAP3 | NM_001195753.2 | c.40T>C | p.Tyr14His | missense_variant | 2/6 | ENST00000054650.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THAP3 | ENST00000054650.9 | c.40T>C | p.Tyr14His | missense_variant | 2/6 | 1 | NM_001195753.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000855 AC: 13AN: 151972Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000646 AC: 9AN: 1392772Hom.: 0 Cov.: 33 AF XY: 0.00000145 AC XY: 1AN XY: 687720
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GnomAD4 genome ? AF: 0.0000855 AC: 13AN: 151972Hom.: 0 Cov.: 32 AF XY: 0.0000674 AC XY: 5AN XY: 74206
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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 | Aug 03, 2022 | The c.40T>C (p.Y14H) alteration is located in exon 2 (coding exon 1) of the THAP3 gene. This alteration results from a T to C substitution at nucleotide position 40, causing the tyrosine (Y) at amino acid position 14 to be replaced by a histidine (H). 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
Pathogenic
D
BayesDel_noAF
Uncertain
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Uncertain
D;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T
M_CAP
Pathogenic
D
MetaRNN
Uncertain
D;D;D
MetaSVM
Pathogenic
D
MutationAssessor
Benign
L;L;L
MutationTaster
Benign
D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D;D;D
REVEL
Uncertain
Sift
Pathogenic
D;D;T
Sift4G
Uncertain
D;D;T
Polyphen
D;D;D
Vest4
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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