chr20-2483588-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_024325.6(ZNF343):c.1373C>T(p.Thr458Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00565 in 1,612,832 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_024325.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF343 | NM_024325.6 | c.1373C>T | p.Thr458Met | missense_variant | 6/6 | ENST00000278772.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF343 | ENST00000278772.9 | c.1373C>T | p.Thr458Met | missense_variant | 6/6 | 2 | NM_024325.6 | P1 | |
ZNF343 | ENST00000612935.4 | c.1496C>T | p.Thr499Met | missense_variant | 8/8 | 5 | |||
ZNF343 | ENST00000617391.4 | c.1103C>T | p.Thr368Met | missense_variant | 4/4 | 4 | |||
ZNF343 | ENST00000465019.1 | n.1401C>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00366 AC: 552AN: 150886Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00359 AC: 902AN: 251446Hom.: 4 AF XY: 0.00372 AC XY: 505AN XY: 135890
GnomAD4 exome AF: 0.00586 AC: 8565AN: 1461834Hom.: 28 Cov.: 32 AF XY: 0.00565 AC XY: 4112AN XY: 727216
GnomAD4 genome AF: 0.00366 AC: 552AN: 150998Hom.: 1 Cov.: 33 AF XY: 0.00350 AC XY: 258AN XY: 73728
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | ZNF343: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at