19-11948769-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_144566.3(ZNF700):c.745C>T(p.Pro249Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,611,244 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_144566.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF700 | NM_144566.3 | c.745C>T | p.Pro249Ser | missense_variant | 4/4 | ENST00000254321.10 | NP_653167.1 | |
ZNF700 | NM_001271848.2 | c.754C>T | p.Pro252Ser | missense_variant | 4/4 | NP_001258777.1 | ||
ZNF69 | XM_017027231.2 | c.500-31272C>T | intron_variant | XP_016882720.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF700 | ENST00000254321.10 | c.745C>T | p.Pro249Ser | missense_variant | 4/4 | 1 | NM_144566.3 | ENSP00000254321.4 | ||
ENSG00000267179 | ENST00000590798.1 | c.63+23496C>T | intron_variant | 2 | ENSP00000467286.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152158Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 247872Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134086
GnomAD4 exome AF: 0.0000398 AC: 58AN: 1459086Hom.: 1 Cov.: 32 AF XY: 0.0000262 AC XY: 19AN XY: 725858
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152158Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 06, 2023 | The c.745C>T (p.P249S) alteration is located in exon 4 (coding exon 4) of the ZNF700 gene. This alteration results from a C to T substitution at nucleotide position 745, causing the proline (P) at amino acid position 249 to be replaced by a serine (S). 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