chr12-71674387-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_031435.4(THAP2):āc.256A>Gā(p.Ile86Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000859 in 1,605,856 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_031435.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THAP2 | NM_031435.4 | c.256A>G | p.Ile86Val | missense_variant | 2/3 | ENST00000308086.3 | |
LOC124902965 | XR_007063367.1 | n.144-2605T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THAP2 | ENST00000308086.3 | c.256A>G | p.Ile86Val | missense_variant | 2/3 | 1 | NM_031435.4 | P1 | |
THAP2 | ENST00000551488.5 | c.40A>G | p.Ile14Val | missense_variant | 2/3 | 3 | |||
THAP2 | ENST00000551238.1 | c.40A>G | p.Ile14Val | missense_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152074Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000121 AC: 30AN: 247888Hom.: 0 AF XY: 0.000142 AC XY: 19AN XY: 134054
GnomAD4 exome AF: 0.0000846 AC: 123AN: 1453782Hom.: 1 Cov.: 33 AF XY: 0.0000899 AC XY: 65AN XY: 722684
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152074Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74286
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 26, 2022 | The c.256A>G (p.I86V) alteration is located in exon 2 (coding exon 2) of the THAP2 gene. This alteration results from a A to G substitution at nucleotide position 256, causing the isoleucine (I) at amino acid position 86 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