16-30571587-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145271.4(ZNF688):c.43G>A(p.Glu15Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000286 in 1,541,040 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_145271.4 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 |
---|---|---|---|---|---|---|---|
ZNF688 | NM_145271.4 | c.43G>A | p.Glu15Lys | missense_variant | 1/3 | ENST00000223459.11 | |
ZNF688 | XM_047433653.1 | c.43G>A | p.Glu15Lys | missense_variant | 1/2 | ||
ZNF688 | NM_001024683.2 | c.155-464G>A | intron_variant | ||||
ZNF688 | XM_047433654.1 | c.155-464G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF688 | ENST00000223459.11 | c.43G>A | p.Glu15Lys | missense_variant | 1/3 | 1 | NM_145271.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000177 AC: 27AN: 152190Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000917 AC: 13AN: 141826Hom.: 0 AF XY: 0.0000774 AC XY: 6AN XY: 77560
GnomAD4 exome AF: 0.0000122 AC: 17AN: 1388850Hom.: 0 Cov.: 31 AF XY: 0.0000117 AC XY: 8AN XY: 685728
GnomAD4 genome AF: 0.000177 AC: 27AN: 152190Hom.: 1 Cov.: 32 AF XY: 0.000256 AC XY: 19AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2022 | The c.43G>A (p.E15K) alteration is located in exon 1 (coding exon 1) of the ZNF688 gene. This alteration results from a G to A substitution at nucleotide position 43, causing the glutamic acid (E) at amino acid position 15 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