chr10-47367970-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_153034.4(ZNF488):c.860C>T(p.Thr287Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000694 in 1,614,132 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 7/10 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153034.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF488 | NM_153034.4 | c.860C>T | p.Thr287Met | missense_variant | 2/2 | ENST00000585316.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF488 | ENST00000585316.3 | c.860C>T | p.Thr287Met | missense_variant | 2/2 | 1 | NM_153034.4 | A2 | |
ZNF488 | ENST00000591025.1 | c.539C>T | p.Thr180Met | missense_variant | 3/3 | 1 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152154Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251158Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135778
GnomAD4 exome AF: 0.0000732 AC: 107AN: 1461860Hom.: 0 Cov.: 30 AF XY: 0.0000619 AC XY: 45AN XY: 727228
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152272Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 10, 2021 | The c.860C>T (p.T287M) alteration is located in exon 2 (coding exon 1) of the ZNF488 gene. This alteration results from a C to T substitution at nucleotide position 860, causing the threonine (T) at amino acid position 287 to be replaced by a methionine (M). 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