chr6-29672930-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBS2_Supporting
The NM_001109809.5(ZFP57):c.1181G>A(p.Ser394Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,612,898 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001109809.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZFP57 | NM_001109809.5 | c.1181G>A | p.Ser394Asn | missense_variant | 5/5 | ENST00000376883.2 | |
ZFP57 | NM_001366333.2 | c.965G>A | p.Ser322Asn | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFP57 | ENST00000376883.2 | c.1181G>A | p.Ser394Asn | missense_variant | 5/5 | 5 | NM_001109809.5 | P1 | |
ZFP57 | ENST00000488757.6 | c.965G>A | p.Ser322Asn | missense_variant | 4/4 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000245 AC: 6AN: 244692Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133914
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1460772Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 726704
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74300
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 05, 2023 | The c.1181G>A (p.S394N) alteration is located in exon 4 (coding exon 4) of the ZFP57 gene. This alteration results from a G to A substitution at nucleotide position 1181, causing the serine (S) at amino acid position 394 to be replaced by an asparagine (N). 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