5-122152507-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_207317.3(ZNF474):c.517C>T(p.Arg173Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000551 in 1,614,058 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R173H) has been classified as Likely benign.
Frequency
Consequence
NM_207317.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF474 | NM_207317.3 | c.517C>T | p.Arg173Cys | missense_variant | 2/2 | ENST00000296600.5 | NP_997200.1 | |
ZNF474-AS1 | XR_007058915.1 | n.272-1904G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF474 | ENST00000296600.5 | c.517C>T | p.Arg173Cys | missense_variant | 2/2 | 1 | NM_207317.3 | ENSP00000296600 | ||
ENST00000504829.1 | n.233+2117G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000439 AC: 11AN: 250640Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135434
GnomAD4 exome AF: 0.0000554 AC: 81AN: 1461884Hom.: 0 Cov.: 30 AF XY: 0.0000509 AC XY: 37AN XY: 727244
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 24, 2024 | The c.517C>T (p.R173C) alteration is located in exon 2 (coding exon 1) of the ZNF474 gene. This alteration results from a C to T substitution at nucleotide position 517, causing the arginine (R) at amino acid position 173 to be replaced by a cysteine (C). 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