chr1-52238582-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004799.4(ZFYVE9):c.1165A>G(p.Met389Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,972 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004799.4 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 | UniProt |
---|---|---|---|---|---|---|---|
ZFYVE9 | NM_004799.4 | c.1165A>G | p.Met389Val | missense_variant | 4/19 | ENST00000287727.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFYVE9 | ENST00000287727.8 | c.1165A>G | p.Met389Val | missense_variant | 4/19 | 5 | NM_004799.4 | P1 | |
ZFYVE9 | ENST00000371591.2 | c.1165A>G | p.Met389Val | missense_variant | 5/20 | 1 | P1 | ||
ZFYVE9 | ENST00000357206.6 | c.1165A>G | p.Met389Val | missense_variant | 4/18 | 1 | |||
ZFYVE9 | ENST00000361625.5 | n.1337A>G | non_coding_transcript_exon_variant | 4/5 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152210Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461762Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727178
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 13, 2022 | The c.1165A>G (p.M389V) alteration is located in exon 4 (coding exon 2) of the ZFYVE9 gene. This alteration results from a A to G substitution at nucleotide position 1165, causing the methionine (M) at amino acid position 389 to be replaced by a valine (V). 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