19-58053434-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_182572.4(ZSCAN1):c.610C>T(p.Arg204Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000404 in 1,608,990 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. R204Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_182572.4 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 | UniProt |
---|---|---|---|---|---|---|---|
ZSCAN1 | NM_182572.4 | c.610C>T | p.Arg204Trp | missense_variant | 6/6 | ENST00000282326.6 | |
ZSCAN1 | XM_006723149.3 | c.730C>T | p.Arg244Trp | missense_variant | 5/5 | ||
ZSCAN1 | XM_047438630.1 | c.331C>T | p.Arg111Trp | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZSCAN1 | ENST00000282326.6 | c.610C>T | p.Arg204Trp | missense_variant | 6/6 | 2 | NM_182572.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152108Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000363 AC: 9AN: 248268Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134598
GnomAD4 exome AF: 0.0000405 AC: 59AN: 1456882Hom.: 0 Cov.: 31 AF XY: 0.0000373 AC XY: 27AN XY: 723920
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152108Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 26, 2023 | The c.610C>T (p.R204W) alteration is located in exon 6 (coding exon 4) of the ZSCAN1 gene. This alteration results from a C to T substitution at nucleotide position 610, causing the arginine (R) at amino acid position 204 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