chr1-247100813-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001142572.2(ZNF669):c.698G>A(p.Cys233Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 1,613,658 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 (★).
Frequency
Consequence
NM_001142572.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF669 | ENST00000448299.7 | c.698G>A | p.Cys233Tyr | missense_variant | Exon 4 of 4 | 1 | NM_001142572.2 | ENSP00000404370.2 | ||
ZNF669 | ENST00000343381.10 | c.956G>A | p.Cys319Tyr | missense_variant | Exon 4 of 4 | 1 | ENSP00000342818.6 | |||
ZNF669 | ENST00000366500.5 | c.*421G>A | downstream_gene_variant | 3 | ENSP00000355456.1 | |||||
ZNF669 | ENST00000366501.1 | c.*508G>A | downstream_gene_variant | 3 | ENSP00000355457.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250968Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135652
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461486Hom.: 0 Cov.: 32 AF XY: 0.0000220 AC XY: 16AN XY: 727026
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152172Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.956G>A (p.C319Y) alteration is located in exon 4 (coding exon 4) of the ZNF669 gene. This alteration results from a G to A substitution at nucleotide position 956, causing the cysteine (C) at amino acid position 319 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