14-67766358-C-T
Variant summary
Our verdict is Benign. The variant received -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_015346.4(ZFYVE26):c.5880G>A(p.Arg1960Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,854 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 Likely benign (★★).
Frequency
Consequence
NM_015346.4 synonymous
Scores
Clinical Significance
Conservation
Publications
- hereditary spastic paraplegia 15Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Myriad Women’s Health, G2P
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ACMG classification
Our verdict: Benign. The variant received -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZFYVE26 | NM_015346.4 | c.5880G>A | p.Arg1960Arg | synonymous_variant | Exon 32 of 42 | ENST00000347230.9 | NP_056161.2 | |
ZFYVE26 | XM_047431173.1 | c.5880G>A | p.Arg1960Arg | synonymous_variant | Exon 32 of 42 | XP_047287129.1 | ||
ZFYVE26 | XM_047431174.1 | c.3555G>A | p.Arg1185Arg | synonymous_variant | Exon 21 of 31 | XP_047287130.1 | ||
ZFYVE26 | XM_047431175.1 | c.3462G>A | p.Arg1154Arg | synonymous_variant | Exon 21 of 31 | XP_047287131.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD2 exomes AF: 0.0000159 AC: 4AN: 251278 AF XY: 0.0000221 show subpopulations
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460854Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 726724 show subpopulations
Age Distribution
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Spastic paraplegia Benign:1
- -
not provided Benign:1
ZFYVE26: BP4, BP7 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at