rs12891164
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_015346.4(ZFYVE26):c.2112T>G(p.Pro704=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,613,750 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P704P) has been classified as Benign.
Frequency
Consequence
NM_015346.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZFYVE26 | NM_015346.4 | c.2112T>G | p.Pro704= | synonymous_variant | 11/42 | ENST00000347230.9 | |
ZFYVE26 | XM_047431173.1 | c.2112T>G | p.Pro704= | synonymous_variant | 11/42 | ||
ZFYVE26 | XM_011536609.3 | c.2112T>G | p.Pro704= | synonymous_variant | 11/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFYVE26 | ENST00000347230.9 | c.2112T>G | p.Pro704= | synonymous_variant | 11/42 | 1 | NM_015346.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151950Hom.: 0 Cov.: 31
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461800Hom.: 0 Cov.: 80 AF XY: 0.00 AC XY: 0AN XY: 727190
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151950Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74206
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at