chr10-119914716-AT-A
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_007190.4(SEC23IP):c.1313-6del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000871 in 1,608,152 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0000082 ( 0 hom. )
Consequence
SEC23IP
NM_007190.4 splice_polypyrimidine_tract, intron
NM_007190.4 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.240
Genes affected
SEC23IP (HGNC:17018): (SEC23 interacting protein) This gene encodes a member of the phosphatidic acid preferring-phospholipase A1 family. The encoded protein is localized to endoplasmic reticulum exit sites and plays a critical role in ER-Golgi transport as part of the multimeric coat protein II complex. An orthologous gene in frogs is required for normal neural crest cell development, suggesting that this gene may play a role in Waardenburg syndrome neural crest defects. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEC23IP | NM_007190.4 | c.1313-6del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000369075.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEC23IP | ENST00000369075.8 | c.1313-6del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_007190.4 | P4 | |||
SEC23IP | ENST00000446561.1 | c.425-6del | splice_polypyrimidine_tract_variant, intron_variant | 3 | |||||
SEC23IP | ENST00000705471.1 | c.1313-6del | splice_polypyrimidine_tract_variant, intron_variant | A1 | |||||
SEC23IP | ENST00000462222.1 | n.225del | non_coding_transcript_exon_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151954Hom.: 0 Cov.: 30
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GnomAD4 exome AF: 0.00000824 AC: 12AN: 1456198Hom.: 0 Cov.: 30 AF XY: 0.00000690 AC XY: 5AN XY: 724792
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GnomAD4 genome AF: 0.0000132 AC: 2AN: 151954Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 74210
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ClinVar
Not reported inComputational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at