19-9467032-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152476.3(ZNF560):c.1915G>A(p.Val639Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,612,062 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. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152476.3 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 |
---|---|---|---|---|---|---|---|
ZNF560 | NM_152476.3 | c.1915G>A | p.Val639Ile | missense_variant | 10/10 | ENST00000301480.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF560 | ENST00000301480.5 | c.1915G>A | p.Val639Ile | missense_variant | 10/10 | 1 | NM_152476.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000200 AC: 3AN: 150362Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251156Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135742
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461700Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727146
GnomAD4 genome AF: 0.0000200 AC: 3AN: 150362Hom.: 0 Cov.: 32 AF XY: 0.0000273 AC XY: 2AN XY: 73368
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at