chr6-29672828-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001109809.5(ZFP57):āc.1283T>Cā(p.Val428Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,612,942 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001109809.5 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 | UniProt |
---|---|---|---|---|---|---|---|
ZFP57 | NM_001109809.5 | c.1283T>C | p.Val428Ala | missense_variant | 5/5 | ENST00000376883.2 | |
ZFP57 | NM_001366333.2 | c.1067T>C | p.Val356Ala | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFP57 | ENST00000376883.2 | c.1283T>C | p.Val428Ala | missense_variant | 5/5 | 5 | NM_001109809.5 | P1 | |
ZFP57 | ENST00000488757.6 | c.1067T>C | p.Val356Ala | missense_variant | 4/4 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000817 AC: 2AN: 244652Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 133890
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1460768Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 726698
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74338
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 19, 2022 | The c.1283T>C (p.V428A) alteration is located in exon 4 (coding exon 4) of the ZFP57 gene. This alteration results from a T to C substitution at nucleotide position 1283, causing the valine (V) at amino acid position 428 to be replaced by an alanine (A). 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