rs199630965
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_015346.4(ZFYVE26):āc.991A>Gā(p.Asn331Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000134 in 1,614,208 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. N331N) has been classified as Likely benign.
Frequency
Consequence
NM_015346.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZFYVE26 | NM_015346.4 | c.991A>G | p.Asn331Asp | missense_variant | 6/42 | ENST00000347230.9 | |
ZFYVE26 | XM_047431173.1 | c.991A>G | p.Asn331Asp | missense_variant | 6/42 | ||
ZFYVE26 | XM_011536609.3 | c.991A>G | p.Asn331Asp | missense_variant | 6/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFYVE26 | ENST00000347230.9 | c.991A>G | p.Asn331Asp | missense_variant | 6/42 | 1 | NM_015346.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000763 AC: 192AN: 251480Hom.: 0 AF XY: 0.000537 AC XY: 73AN XY: 135918
GnomAD4 exome AF: 0.000138 AC: 202AN: 1461880Hom.: 1 Cov.: 31 AF XY: 0.000107 AC XY: 78AN XY: 727238
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152328Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74496
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 05, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Spastic paraplegia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Hereditary spastic paraplegia 15 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jul 07, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at