5-80437865-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001284236.3(ZFYVE16):c.1180C>T(p.Arg394Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,613,726 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R394Q) has been classified as Benign.
Frequency
Consequence
NM_001284236.3 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 |
---|---|---|---|---|---|---|---|
ZFYVE16 | NM_001284236.3 | c.1180C>T | p.Arg394Trp | missense_variant | 4/19 | ENST00000505560.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFYVE16 | ENST00000505560.5 | c.1180C>T | p.Arg394Trp | missense_variant | 4/19 | 1 | NM_001284236.3 | P1 | |
FAM151B-DT | ENST00000666568.1 | n.259-23398G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000461 AC: 7AN: 151936Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000758 AC: 19AN: 250814Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135534
GnomAD4 exome AF: 0.0000335 AC: 49AN: 1461790Hom.: 0 Cov.: 66 AF XY: 0.0000316 AC XY: 23AN XY: 727184
GnomAD4 genome ? AF: 0.0000461 AC: 7AN: 151936Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74190
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 20, 2023 | The c.1180C>T (p.R394W) alteration is located in exon 4 (coding exon 2) of the ZFYVE16 gene. This alteration results from a C to T substitution at nucleotide position 1180, causing the arginine (R) at amino acid position 394 to be replaced by a tryptophan (W). 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