1-247100850-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001142572.2(ZNF669):c.661G>A(p.Glu221Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,613,986 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_001142572.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF669 | ENST00000448299.7 | c.661G>A | p.Glu221Lys | missense_variant | Exon 4 of 4 | 1 | NM_001142572.2 | ENSP00000404370.2 | ||
ZNF669 | ENST00000343381.10 | c.919G>A | p.Glu307Lys | missense_variant | Exon 4 of 4 | 1 | ENSP00000342818.6 | |||
ZNF669 | ENST00000366500.5 | c.*384G>A | downstream_gene_variant | 3 | ENSP00000355456.1 | |||||
ZNF669 | ENST00000366501.1 | c.*471G>A | downstream_gene_variant | 3 | ENSP00000355457.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251328Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135844
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461814Hom.: 0 Cov.: 32 AF XY: 0.0000248 AC XY: 18AN XY: 727186
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152172Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.919G>A (p.E307K) 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 919, causing the glutamic acid (E) at amino acid position 307 to be replaced by a lysine (K). 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