14-67767822-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015346.4(ZFYVE26):c.5672A>C(p.Asn1891Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/19 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. N1891S) has been classified as Benign.
Frequency
Consequence
NM_015346.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZFYVE26 | NM_015346.4 | c.5672A>C | p.Asn1891Thr | missense_variant | Exon 31 of 42 | ENST00000347230.9 | NP_056161.2 | |
ZFYVE26 | XM_047431173.1 | c.5672A>C | p.Asn1891Thr | missense_variant | Exon 31 of 42 | XP_047287129.1 | ||
ZFYVE26 | XM_047431174.1 | c.3347A>C | p.Asn1116Thr | missense_variant | Exon 20 of 31 | XP_047287130.1 | ||
ZFYVE26 | XM_047431175.1 | c.3254A>C | p.Asn1085Thr | missense_variant | Exon 20 of 31 | XP_047287131.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 68
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at