14-72997835-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_021260.4(ZFYVE1):c.964G>A(p.Val322Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000131 in 1,598,416 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021260.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZFYVE1 | ENST00000556143.6 | c.964G>A | p.Val322Met | missense_variant | Exon 3 of 12 | 1 | NM_021260.4 | ENSP00000450742.1 | ||
ZFYVE1 | ENST00000318876.9 | c.964G>A | p.Val322Met | missense_variant | Exon 3 of 12 | 1 | ENSP00000326921.5 | |||
ZFYVE1 | ENST00000553891.5 | c.964G>A | p.Val322Met | missense_variant | Exon 3 of 13 | 5 | ENSP00000452442.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152126Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248058Hom.: 0 AF XY: 0.00000747 AC XY: 1AN XY: 133932
GnomAD4 exome AF: 0.0000111 AC: 16AN: 1446172Hom.: 0 Cov.: 31 AF XY: 0.00000838 AC XY: 6AN XY: 716026
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152244Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74420
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.964G>A (p.V322M) alteration is located in exon 3 (coding exon 2) of the ZFYVE1 gene. This alteration results from a G to A substitution at nucleotide position 964, causing the valine (V) at amino acid position 322 to be replaced by a methionine (M). 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