chr5-178931711-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_030613.4(ZFP2):āc.398A>Gā(p.Asn133Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,613,984 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_030613.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZFP2 | NM_030613.4 | c.398A>G | p.Asn133Ser | missense_variant | 5/5 | ENST00000361362.7 | NP_085116.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZFP2 | ENST00000361362.7 | c.398A>G | p.Asn133Ser | missense_variant | 5/5 | 1 | NM_030613.4 | ENSP00000354453 | P1 | |
ZFP2 | ENST00000523286.1 | c.398A>G | p.Asn133Ser | missense_variant | 5/5 | 1 | ENSP00000430531 | P1 | ||
ZFP2 | ENST00000520301.5 | c.398A>G | p.Asn133Ser | missense_variant | 4/4 | 5 | ENSP00000430980 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461776Hom.: 0 Cov.: 38 AF XY: 0.0000110 AC XY: 8AN XY: 727172
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 25, 2023 | The c.398A>G (p.N133S) alteration is located in exon 5 (coding exon 1) of the ZFP2 gene. This alteration results from a A to G substitution at nucleotide position 398, causing the asparagine (N) at amino acid position 133 to be replaced by a serine (S). 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