chr19-57676158-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152677.4(ZSCAN4):c.13C>A(p.Leu5Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000069 in 1,609,730 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 (★).
Frequency
Consequence
NM_152677.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZSCAN4 | NM_152677.4 | c.13C>A | p.Leu5Ile | missense_variant | 3/5 | ENST00000318203.9 | |
ZSCAN4 | NM_001384833.1 | c.13C>A | p.Leu5Ile | missense_variant | 5/7 | ||
ZSCAN4 | XM_017026458.1 | c.13C>A | p.Leu5Ile | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZSCAN4 | ENST00000318203.9 | c.13C>A | p.Leu5Ile | missense_variant | 3/5 | 2 | NM_152677.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000282 AC: 7AN: 248380Hom.: 0 AF XY: 0.0000446 AC XY: 6AN XY: 134470
GnomAD4 exome AF: 0.0000741 AC: 108AN: 1457598Hom.: 0 Cov.: 31 AF XY: 0.0000800 AC XY: 58AN XY: 724980
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 22, 2022 | The c.13C>A (p.L5I) alteration is located in exon 3 (coding exon 1) of the ZSCAN4 gene. This alteration results from a C to A substitution at nucleotide position 13, causing the leucine (L) at amino acid position 5 to be replaced by an isoleucine (I). 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