19-57678762-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152677.4(ZSCAN4):c.1159G>C(p.Glu387Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000121 in 1,613,978 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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. E387K) has been classified as Likely benign.
Frequency
Consequence
NM_152677.4 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 |
---|---|---|---|---|---|---|---|
ZSCAN4 | NM_152677.4 | c.1159G>C | p.Glu387Gln | missense_variant | 5/5 | ENST00000318203.9 | |
ZSCAN4 | NM_001384833.1 | c.1159G>C | p.Glu387Gln | missense_variant | 7/7 | ||
ZSCAN4 | XM_017026458.1 | c.1159G>C | p.Glu387Gln | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZSCAN4 | ENST00000318203.9 | c.1159G>C | p.Glu387Gln | missense_variant | 5/5 | 2 | NM_152677.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152100Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251460Hom.: 0 AF XY: 0.0000809 AC XY: 11AN XY: 135898
GnomAD4 exome AF: 0.000127 AC: 186AN: 1461878Hom.: 0 Cov.: 32 AF XY: 0.000125 AC XY: 91AN XY: 727240
GnomAD4 genome ? AF: 0.0000592 AC: 9AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2022 | The c.1159G>C (p.E387Q) alteration is located in exon 5 (coding exon 3) of the ZSCAN4 gene. This alteration results from a G to C substitution at nucleotide position 1159, causing the glutamic acid (E) at amino acid position 387 to be replaced by a glutamine (Q). 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