14-67766358-C-G
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015346.4(ZFYVE26):c.5880G>C(p.Arg1960Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,460,854 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar. Synonymous variant affecting the same amino acid position (i.e. R1960R) has been classified as Likely benign.
Frequency
Consequence
NM_015346.4 missense
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: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZFYVE26 | NM_015346.4 | c.5880G>C | p.Arg1960Ser | missense_variant | Exon 32 of 42 | ENST00000347230.9 | NP_056161.2 | |
ZFYVE26 | XM_047431173.1 | c.5880G>C | p.Arg1960Ser | missense_variant | Exon 32 of 42 | XP_047287129.1 | ||
ZFYVE26 | XM_047431174.1 | c.3555G>C | p.Arg1185Ser | missense_variant | Exon 21 of 31 | XP_047287130.1 | ||
ZFYVE26 | XM_047431175.1 | c.3462G>C | p.Arg1154Ser | missense_variant | Exon 21 of 31 | XP_047287131.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD2 exomes AF: 0.00000398 AC: 1AN: 251278 AF XY: 0.00000736 show subpopulations
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1460854Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 726724 show subpopulations
Age Distribution
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at