14-72993318-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_021260.4(ZFYVE1):c.1028G>A(p.Arg343Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000274 in 1,461,826 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZFYVE1 | ENST00000556143.6 | c.1028G>A | p.Arg343Gln | missense_variant | Exon 4 of 12 | 1 | NM_021260.4 | ENSP00000450742.1 | ||
ZFYVE1 | ENST00000318876.9 | c.1028G>A | p.Arg343Gln | missense_variant | Exon 4 of 12 | 1 | ENSP00000326921.5 | |||
ZFYVE1 | ENST00000553891.5 | c.1028G>A | p.Arg343Gln | missense_variant | Exon 4 of 13 | 5 | ENSP00000452442.1 |
Frequencies
GnomAD3 genomes Cov.: 28
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251416Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135896
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461826Hom.: 0 Cov.: 34 AF XY: 0.00000413 AC XY: 3AN XY: 727220
GnomAD4 genome Cov.: 28
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1028G>A (p.R343Q) alteration is located in exon 4 (coding exon 3) of the ZFYVE1 gene. This alteration results from a G to A substitution at nucleotide position 1028, causing the arginine (R) at amino acid position 343 to be replaced by a glutamine (Q). 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