4-2304548-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020972.3(ZFYVE28):c.1792G>T(p.Gly598Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000298 in 1,612,580 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020972.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZFYVE28 | NM_020972.3 | c.1792G>T | p.Gly598Cys | missense_variant | 8/13 | ENST00000290974.7 | |
ZFYVE28 | NM_001172656.2 | c.1702G>T | p.Gly568Cys | missense_variant | 7/12 | ||
ZFYVE28 | NM_001172659.2 | c.1582G>T | p.Gly528Cys | missense_variant | 8/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFYVE28 | ENST00000290974.7 | c.1792G>T | p.Gly598Cys | missense_variant | 8/13 | 1 | NM_020972.3 | P2 | |
ENST00000510632.1 | n.263-2343C>A | intron_variant, non_coding_transcript_variant | 4 | ||||||
ZFYVE28 | ENST00000511071.5 | c.1702G>T | p.Gly568Cys | missense_variant | 7/12 | 5 | A2 | ||
ZFYVE28 | ENST00000515312.5 | c.1582G>T | p.Gly528Cys | missense_variant | 8/13 | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152248Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000443 AC: 11AN: 248072Hom.: 0 AF XY: 0.0000593 AC XY: 8AN XY: 134890
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1460332Hom.: 0 Cov.: 38 AF XY: 0.0000358 AC XY: 26AN XY: 726436
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152248Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2022 | The c.1792G>T (p.G598C) alteration is located in exon 8 (coding exon 8) of the ZFYVE28 gene. This alteration results from a G to T substitution at nucleotide position 1792, causing the glycine (G) at amino acid position 598 to be replaced by a cysteine (C). 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