16-31061463-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024706.5(ZNF668):c.1465G>A(p.Ala489Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,652 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024706.5 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 |
---|---|---|---|---|---|---|---|
ZNF668 | NM_024706.5 | c.1465G>A | p.Ala489Thr | missense_variant | 3/3 | ENST00000300849.5 | |
ZNF668 | NM_001172669.2 | c.1534G>A | p.Ala512Thr | missense_variant | 4/4 | ||
ZNF668 | NM_001172668.2 | c.1465G>A | p.Ala489Thr | missense_variant | 3/3 | ||
ZNF668 | NM_001172670.2 | c.1465G>A | p.Ala489Thr | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF668 | ENST00000300849.5 | c.1465G>A | p.Ala489Thr | missense_variant | 3/3 | 1 | NM_024706.5 | P1 | |
ENST00000622229.1 | n.2040C>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250692Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135718
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461472Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 727082
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2022 | The c.1534G>A (p.A512T) alteration is located in exon 4 (coding exon 3) of the ZNF668 gene. This alteration results from a G to A substitution at nucleotide position 1534, causing the alanine (A) at amino acid position 512 to be replaced by a threonine (T). 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