chr20-2483283-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024325.6(ZNF343):c.1678C>T(p.Arg560Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000484 in 1,610,352 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R560Q) has been classified as Likely benign.
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.1678C>T | p.Arg560Trp | missense_variant | 6/6 | ENST00000278772.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF343 | ENST00000278772.9 | c.1678C>T | p.Arg560Trp | missense_variant | 6/6 | 2 | NM_024325.6 | P1 | |
ZNF343 | ENST00000612935.4 | c.1801C>T | p.Arg601Trp | missense_variant | 8/8 | 5 | |||
ZNF343 | ENST00000617391.4 | c.1408C>T | p.Arg470Trp | missense_variant | 4/4 | 4 | |||
ZNF343 | ENST00000465019.1 | n.1706C>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000867 AC: 13AN: 150018Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250876Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135552
GnomAD4 exome AF: 0.0000445 AC: 65AN: 1460334Hom.: 0 Cov.: 32 AF XY: 0.0000440 AC XY: 32AN XY: 726502
GnomAD4 genome AF: 0.0000867 AC: 13AN: 150018Hom.: 0 Cov.: 32 AF XY: 0.0000820 AC XY: 6AN XY: 73136
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 26, 2023 | The c.1678C>T (p.R560W) alteration is located in exon 6 (coding exon 4) of the ZNF343 gene. This alteration results from a C to T substitution at nucleotide position 1678, causing the arginine (R) at amino acid position 560 to be replaced by a tryptophan (W). 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