16-31061166-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_024706.5(ZNF668):c.1762C>T(p.Arg588Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000382 in 1,517,896 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. R588H) has been classified as Uncertain significance.
Frequency
Consequence
NM_024706.5 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 |
---|---|---|---|---|---|---|---|
ZNF668 | NM_024706.5 | c.1762C>T | p.Arg588Cys | missense_variant | 3/3 | ENST00000300849.5 | |
ZNF668 | NM_001172669.2 | c.1831C>T | p.Arg611Cys | missense_variant | 4/4 | ||
ZNF668 | NM_001172668.2 | c.1762C>T | p.Arg588Cys | missense_variant | 3/3 | ||
ZNF668 | NM_001172670.2 | c.1762C>T | p.Arg588Cys | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF668 | ENST00000300849.5 | c.1762C>T | p.Arg588Cys | missense_variant | 3/3 | 1 | NM_024706.5 | P1 | |
ENST00000622229.1 | n.1743G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000164 AC: 29AN: 177340Hom.: 0 AF XY: 0.0000859 AC XY: 8AN XY: 93160
GnomAD4 exome AF: 0.0000381 AC: 52AN: 1365722Hom.: 0 Cov.: 30 AF XY: 0.0000299 AC XY: 20AN XY: 669004
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2021 | The c.1831C>T (p.R611C) alteration is located in exon 4 (coding exon 3) of the ZNF668 gene. This alteration results from a C to T substitution at nucleotide position 1831, causing the arginine (R) at amino acid position 611 to be replaced by a cysteine (C). 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