1-52238118-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004799.4(ZFYVE9):c.701C>T(p.Ser234Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000075 in 1,613,982 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_004799.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZFYVE9 | NM_004799.4 | c.701C>T | p.Ser234Phe | missense_variant | 4/19 | ENST00000287727.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFYVE9 | ENST00000287727.8 | c.701C>T | p.Ser234Phe | missense_variant | 4/19 | 5 | NM_004799.4 | P1 | |
ZFYVE9 | ENST00000371591.2 | c.701C>T | p.Ser234Phe | missense_variant | 5/20 | 1 | P1 | ||
ZFYVE9 | ENST00000357206.6 | c.701C>T | p.Ser234Phe | missense_variant | 4/18 | 1 | |||
ZFYVE9 | ENST00000361625.5 | n.873C>T | non_coding_transcript_exon_variant | 4/5 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250798Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135486
GnomAD4 exome AF: 0.0000794 AC: 116AN: 1461806Hom.: 0 Cov.: 32 AF XY: 0.0000853 AC XY: 62AN XY: 727210
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 29, 2023 | The c.701C>T (p.S234F) alteration is located in exon 4 (coding exon 2) of the ZFYVE9 gene. This alteration results from a C to T substitution at nucleotide position 701, causing the serine (S) at amino acid position 234 to be replaced by a phenylalanine (F). 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