chr2-112230925-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032494.3(ZC3H8):c.869G>A(p.Cys290Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000535 in 1,121,748 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_032494.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZC3H8 | NM_032494.3 | c.869G>A | p.Cys290Tyr | missense_variant | Exon 8 of 9 | ENST00000409573.7 | NP_115883.2 | |
ZC3H8 | XR_001738994.2 | n.930G>A | non_coding_transcript_exon_variant | Exon 8 of 9 | ||||
FBLN7 | XR_007069507.1 | n.10508+40C>T | intron_variant | Intron 8 of 9 | ||||
FBLN7 | XR_007069508.1 | n.10508+40C>T | intron_variant | Intron 8 of 8 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000237 AC: 2AN: 84308Hom.: 0 AF XY: 0.0000436 AC XY: 2AN XY: 45920
GnomAD4 exome AF: 0.00000535 AC: 6AN: 1121748Hom.: 0 Cov.: 20 AF XY: 0.00000545 AC XY: 3AN XY: 550762
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.869G>A (p.C290Y) alteration is located in exon 8 (coding exon 8) of the ZC3H8 gene. This alteration results from a G to A substitution at nucleotide position 869, causing the cysteine (C) at amino acid position 290 to be replaced by a tyrosine (Y). 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