chr7-108564580-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001130475.3(THAP5):c.799A>C(p.Asn267His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,613,770 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001130475.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THAP5 | NM_001130475.3 | c.799A>C | p.Asn267His | missense_variant | 3/3 | ENST00000415914.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THAP5 | ENST00000415914.4 | c.799A>C | p.Asn267His | missense_variant | 3/3 | 1 | NM_001130475.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152212Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250858Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135714
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461558Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727094
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152212Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 09, 2023 | The c.799A>C (p.N267H) alteration is located in exon 3 (coding exon 3) of the THAP5 gene. This alteration results from a A to C substitution at nucleotide position 799, causing the asparagine (N) at amino acid position 267 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at