chr4-25333385-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_024936.3(ZCCHC4):c.532C>T(p.Arg178Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000359 in 1,613,970 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024936.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZCCHC4 | ENST00000302874.9 | c.532C>T | p.Arg178Trp | missense_variant | Exon 4 of 13 | 1 | NM_024936.3 | ENSP00000303468.4 | ||
ZCCHC4 | ENST00000505451.5 | n.557C>T | non_coding_transcript_exon_variant | Exon 4 of 9 | 1 | |||||
ZCCHC4 | ENST00000507760.5 | n.532C>T | non_coding_transcript_exon_variant | Exon 4 of 9 | 1 | ENSP00000422115.1 | ||||
ZCCHC4 | ENST00000505412.1 | c.124C>T | p.Arg42Trp | missense_variant | Exon 1 of 10 | 3 | ENSP00000422269.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152150Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000321 AC: 8AN: 249506Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135358
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1461820Hom.: 0 Cov.: 31 AF XY: 0.0000358 AC XY: 26AN XY: 727210
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152150Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.532C>T (p.R178W) alteration is located in exon 4 (coding exon 4) of the ZCCHC4 gene. This alteration results from a C to T substitution at nucleotide position 532, causing the arginine (R) at amino acid position 178 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