14-72997817-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_021260.4(ZFYVE1):c.982G>A(p.Gly328Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000012 in 1,586,698 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 Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZFYVE1 | NM_021260.4 | c.982G>A | p.Gly328Ser | missense_variant | Exon 3 of 12 | ENST00000556143.6 | NP_067083.1 | |
ZFYVE1 | NM_001281734.2 | c.982G>A | p.Gly328Ser | missense_variant | Exon 3 of 12 | NP_001268663.1 | ||
ZFYVE1 | XM_047431481.1 | c.982G>A | p.Gly328Ser | missense_variant | Exon 3 of 7 | XP_047287437.1 | ||
ZFYVE1 | XM_047431482.1 | c.-264G>A | 5_prime_UTR_variant | Exon 3 of 12 | XP_047287438.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZFYVE1 | ENST00000556143.6 | c.982G>A | p.Gly328Ser | missense_variant | Exon 3 of 12 | 1 | NM_021260.4 | ENSP00000450742.1 | ||
ZFYVE1 | ENST00000318876.9 | c.982G>A | p.Gly328Ser | missense_variant | Exon 3 of 12 | 1 | ENSP00000326921.5 | |||
ZFYVE1 | ENST00000553891.5 | c.982G>A | p.Gly328Ser | missense_variant | Exon 3 of 13 | 5 | ENSP00000452442.1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152148Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000827 AC: 2AN: 241814Hom.: 0 AF XY: 0.0000153 AC XY: 2AN XY: 130360
GnomAD4 exome AF: 0.00000349 AC: 5AN: 1434550Hom.: 0 Cov.: 31 AF XY: 0.00000565 AC XY: 4AN XY: 708536
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152148Hom.: 0 Cov.: 31 AF XY: 0.0000807 AC XY: 6AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.982G>A (p.G328S) 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 982, causing the glycine (G) at amino acid position 328 to be replaced by a serine (S). 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