7-149207353-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003575.4(ZNF282):c.715G>A(p.Ala239Thr) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000441 in 1,587,890 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003575.4 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
ZNF282 | NM_003575.4 | c.715G>A | p.Ala239Thr | missense_variant, splice_region_variant | 4/8 | ENST00000610704.5 | |
ZNF282 | NM_001303481.3 | c.715G>A | p.Ala239Thr | missense_variant, splice_region_variant | 4/9 | ||
ZNF282 | XM_006716151.5 | c.715G>A | p.Ala239Thr | missense_variant, splice_region_variant | 4/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF282 | ENST00000610704.5 | c.715G>A | p.Ala239Thr | missense_variant, splice_region_variant | 4/8 | 1 | NM_003575.4 | P1 | |
ZNF282 | ENST00000479907.1 | c.715G>A | p.Ala239Thr | missense_variant, splice_region_variant | 4/9 | 2 | |||
ZNF282 | ENST00000462740.1 | n.190G>A | splice_region_variant, non_coding_transcript_exon_variant | 2/2 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000191 AC: 29AN: 152142Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000713 AC: 15AN: 210352Hom.: 0 AF XY: 0.0000619 AC XY: 7AN XY: 113046
GnomAD4 exome AF: 0.0000286 AC: 41AN: 1435630Hom.: 0 Cov.: 31 AF XY: 0.0000253 AC XY: 18AN XY: 711676
GnomAD4 genome AF: 0.000190 AC: 29AN: 152260Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74464
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2021 | The c.715G>A (p.A239T) alteration is located in exon 4 (coding exon 4) of the ZNF282 gene. This alteration results from a G to A substitution at nucleotide position 715, causing the alanine (A) at amino acid position 239 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