chr7-108564681-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001130475.3(THAP5):c.698C>T(p.Ala233Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000164 in 1,613,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THAP5 | NM_001130475.3 | c.698C>T | p.Ala233Val | missense_variant | 3/3 | ENST00000415914.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THAP5 | ENST00000415914.4 | c.698C>T | p.Ala233Val | missense_variant | 3/3 | 1 | NM_001130475.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000177 AC: 27AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000227 AC: 57AN: 250962Hom.: 0 AF XY: 0.000206 AC XY: 28AN XY: 135768
GnomAD4 exome AF: 0.000163 AC: 238AN: 1461624Hom.: 0 Cov.: 31 AF XY: 0.000173 AC XY: 126AN XY: 727130
GnomAD4 genome ? AF: 0.000177 AC: 27AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 10, 2022 | The c.698C>T (p.A233V) alteration is located in exon 3 (coding exon 3) of the THAP5 gene. This alteration results from a C to T substitution at nucleotide position 698, causing the alanine (A) at amino acid position 233 to be replaced by a valine (V). 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