20-2483449-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024325.6(ZNF343):c.1512G>T(p.Gln504His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,460,552 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_024325.6 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 |
---|---|---|---|---|---|---|---|
ZNF343 | NM_024325.6 | c.1512G>T | p.Gln504His | missense_variant | 6/6 | ENST00000278772.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF343 | ENST00000278772.9 | c.1512G>T | p.Gln504His | missense_variant | 6/6 | 2 | NM_024325.6 | P1 | |
ZNF343 | ENST00000612935.4 | c.1635G>T | p.Gln545His | missense_variant | 8/8 | 5 | |||
ZNF343 | ENST00000617391.4 | c.1242G>T | p.Gln414His | missense_variant | 4/4 | 4 | |||
ZNF343 | ENST00000465019.1 | n.1540G>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 9AN: 144974Hom.: 0 Cov.: 32 FAILED QC
GnomAD3 exomes AF: 0.0000400 AC: 10AN: 249730Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135126
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1460552Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 726606
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000620 AC: 9AN: 145086Hom.: 0 Cov.: 32 AF XY: 0.0000564 AC XY: 4AN XY: 70878
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at