chr20-33791116-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP4_ModerateBP6_ModerateBS1
The NM_001282933.2(ZNF341):c.2164C>T(p.Arg722Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000576 in 1,613,346 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R722H) has been classified as Likely benign.
Frequency
Consequence
NM_001282933.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF341 | NM_001282933.2 | c.2164C>T | p.Arg722Cys | missense_variant | 15/15 | ENST00000375200.6 | |
ZNF341-AS1 | NR_110623.1 | n.242-3339G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF341 | ENST00000375200.6 | c.2164C>T | p.Arg722Cys | missense_variant | 15/15 | 1 | NM_001282933.2 | P4 | |
ZNF341-AS1 | ENST00000443171.6 | n.252-3339G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000232 AC: 58AN: 249488Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135356
GnomAD4 exome AF: 0.0000595 AC: 87AN: 1461004Hom.: 0 Cov.: 32 AF XY: 0.0000427 AC XY: 31AN XY: 726826
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152342Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74500
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 24, 2023 | - - |
Long QT syndrome Benign:1
Likely benign, no assertion criteria provided | research | Medical Research Institute, Tokyo Medical and Dental University | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at