chr4-82918158-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024672.6(THAP9):āc.1946A>Gā(p.Asp649Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,614,076 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_024672.6 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 |
---|---|---|---|---|---|---|---|
THAP9 | NM_024672.6 | c.1946A>G | p.Asp649Gly | missense_variant | 5/5 | ENST00000302236.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THAP9 | ENST00000302236.10 | c.1946A>G | p.Asp649Gly | missense_variant | 5/5 | 1 | NM_024672.6 | P1 | |
THAP9 | ENST00000505901.1 | c.*1703A>G | 3_prime_UTR_variant, NMD_transcript_variant | 6/6 | 2 | ||||
LIN54 | ENST00000505905.1 | n.305-4717T>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250882Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135684
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461844Hom.: 0 Cov.: 66 AF XY: 0.00000413 AC XY: 3AN XY: 727222
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 12, 2021 | The c.1946A>G (p.D649G) alteration is located in exon 5 (coding exon 5) of the THAP9 gene. This alteration results from a A to G substitution at nucleotide position 1946, causing the aspartic acid (D) at amino acid position 649 to be replaced by a glycine (G). 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