chr4-2270851-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_020972.3(ZFYVE28):c.2538C>G(p.Phe846Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,440 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZFYVE28 | NM_020972.3 | c.2538C>G | p.Phe846Leu | missense_variant | 13/13 | ENST00000290974.7 | |
ZFYVE28 | NM_001172656.2 | c.2448C>G | p.Phe816Leu | missense_variant | 12/12 | ||
ZFYVE28 | NM_001172659.2 | c.2328C>G | p.Phe776Leu | missense_variant | 13/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFYVE28 | ENST00000290974.7 | c.2538C>G | p.Phe846Leu | missense_variant | 13/13 | 1 | NM_020972.3 | P2 | |
ZFYVE28 | ENST00000508471.5 | c.453C>G | p.Phe151Leu | missense_variant | 7/7 | 1 | A2 | ||
ZFYVE28 | ENST00000511071.5 | c.2448C>G | p.Phe816Leu | missense_variant | 12/12 | 5 | A2 | ||
ZFYVE28 | ENST00000515312.5 | c.2328C>G | p.Phe776Leu | missense_variant | 13/13 | 2 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460440Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726534
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 28, 2022 | The c.2538C>G (p.F846L) alteration is located in exon 13 (coding exon 13) of the ZFYVE28 gene. This alteration results from a C to G substitution at nucleotide position 2538, causing the phenylalanine (F) at amino acid position 846 to be replaced by a leucine (L). 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
Publications
No publications associated with this variant yet.