19-56574646-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001001668.4(ZNF470):āc.196A>Gā(p.Ile66Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000171 in 1,461,040 control chromosomes in the GnomAD database, including 2 homozygotes. 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 (ā ).
Frequency
Consequence
NM_001001668.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF470 | NM_001001668.4 | c.196A>G | p.Ile66Val | missense_variant | 5/6 | ENST00000330619.13 | NP_001001668.3 | |
ZNF470 | XM_047438804.1 | c.196A>G | p.Ile66Val | missense_variant | 6/7 | XP_047294760.1 | ||
ZNF470 | XM_047438805.1 | c.43A>G | p.Ile15Val | missense_variant | 4/5 | XP_047294761.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF470 | ENST00000330619.13 | c.196A>G | p.Ile66Val | missense_variant | 5/6 | 1 | NM_001001668.4 | ENSP00000333223 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000599 AC: 15AN: 250476Hom.: 1 AF XY: 0.0000960 AC XY: 13AN XY: 135442
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461040Hom.: 2 Cov.: 32 AF XY: 0.0000275 AC XY: 20AN XY: 726832
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 05, 2023 | The c.196A>G (p.I66V) alteration is located in exon 5 (coding exon 3) of the ZNF470 gene. This alteration results from a A to G substitution at nucleotide position 196, causing the isoleucine (I) at amino acid position 66 to be replaced by a valine (V). 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