chr20-17957016-G-A
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001282454.2(SNX5):c.-243C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,162 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.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Consequence
SNX5
NM_001282454.2 5_prime_UTR_premature_start_codon_gain
NM_001282454.2 5_prime_UTR_premature_start_codon_gain
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.29
Genes affected
SNX5 (HGNC:14969): (sorting nexin 5) This gene encodes a member of the sorting nexin family. Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. This protein functions in endosomal sorting, the phosphoinositide-signaling pathway, and macropinocytosis. This gene may play a role in the tumorigenesis of papillary thyroid carcinoma. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Sep 2013]
OVOL2 (HGNC:15804): (ovo like zinc finger 2) This gene encodes a member of the evolutionarily conserved ovo-like protein family. Mammalian members of this family contain a single zinc finger domain composed of a tetrad of C2H2 zinc fingers with variable N- and C-terminal extensions that contain intrinsically disordered domains. Members of this family are involved in epithelial development and differentiation. Knockout of this gene in mouse results in early embryonic lethality with phenotypes that include neurectoderm expansion, impaired vascularization, and heart anomalies. In humans, allelic variants of this gene have been associated with posterior polymorphous corneal dystrophy. [provided by RefSeq, Apr 2016]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.31).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| SNX5 | NM_014426.4 | c.73C>T | p.Leu25Leu | synonymous_variant | Exon 2 of 13 | ENST00000377759.9 | NP_055241.1 | |
| SNX5 | NM_001282454.2 | c.-243C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 13 | NP_001269383.1 | |||
| SNX5 | NM_152227.3 | c.73C>T | p.Leu25Leu | synonymous_variant | Exon 3 of 14 | NP_689413.1 | ||
| SNX5 | NM_001282454.2 | c.-243C>T | 5_prime_UTR_variant | Exon 2 of 13 | NP_001269383.1 |
Ensembl
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152162Hom.: 0 Cov.: 32
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GnomAD4 exome Cov.: 27
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GnomAD4 genome 0.00000657 AC: 1AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74328
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at