rs10748180
Positions:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_031435.4(THAP2):c.*157A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000744 in 660,184 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00083 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00072 ( 1 hom. )
Consequence
THAP2
NM_031435.4 3_prime_UTR
NM_031435.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.69
Genes affected
THAP2 (HGNC:20854): (THAP domain containing 2) Predicted to enable DNA binding activity and metal ion binding activity. Located in nucleolus. [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 (BayesDel_noAF=-0.92).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THAP2 | NM_031435.4 | c.*157A>C | 3_prime_UTR_variant | 3/3 | ENST00000308086.3 | ||
LOC124902965 | XR_007063367.1 | n.144-5483T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THAP2 | ENST00000308086.3 | c.*157A>C | 3_prime_UTR_variant | 3/3 | 1 | NM_031435.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000835 AC: 127AN: 152042Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.000717 AC: 364AN: 508024Hom.: 1 Cov.: 7 AF XY: 0.000796 AC XY: 200AN XY: 251234
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GnomAD4 genome ? AF: 0.000835 AC: 127AN: 152160Hom.: 0 Cov.: 33 AF XY: 0.000780 AC XY: 58AN XY: 74390
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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