14-72993312-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.1034G>A(p.Arg345Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000601 in 1,613,224 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict 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.1034G>A | p.Arg345Gln | missense_variant | Exon 4 of 12 | 1 | NM_021260.4 | ENSP00000450742.1 | ||
ZFYVE1 | ENST00000318876.9 | c.1034G>A | p.Arg345Gln | missense_variant | Exon 4 of 12 | 1 | ENSP00000326921.5 | |||
ZFYVE1 | ENST00000553891.5 | c.1034G>A | p.Arg345Gln | missense_variant | Exon 4 of 13 | 5 | ENSP00000452442.1 |
Frequencies
GnomAD3 genomes AF: 0.0000528 AC: 8AN: 151382Hom.: 0 Cov.: 28
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251448Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135912
GnomAD4 exome AF: 0.0000609 AC: 89AN: 1461842Hom.: 0 Cov.: 34 AF XY: 0.0000564 AC XY: 41AN XY: 727222
GnomAD4 genome AF: 0.0000528 AC: 8AN: 151382Hom.: 0 Cov.: 28 AF XY: 0.0000406 AC XY: 3AN XY: 73864
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1034G>A (p.R345Q) 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 1034, causing the arginine (R) at amino acid position 345 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