chr10-119914716-A-AT
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_007190.4(SEC23IP):c.1313-6dup 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 0.114 in 1,608,142 control chromosomes in the GnomAD database, including 11,058 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.11 ( 943 hom., cov: 30)
Exomes 𝑓: 0.11 ( 10115 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 Benign. Variant got -8 ACMG points.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEC23IP | NM_007190.4 | c.1313-6dup | splice_polypyrimidine_tract_variant, intron_variant | ENST00000369075.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEC23IP | ENST00000369075.8 | c.1313-6dup | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_007190.4 | P4 | |||
SEC23IP | ENST00000446561.1 | c.425-6dup | splice_polypyrimidine_tract_variant, intron_variant | 3 | |||||
SEC23IP | ENST00000705471.1 | c.1313-6dup | splice_polypyrimidine_tract_variant, intron_variant | A1 | |||||
SEC23IP | ENST00000462222.1 | n.225dup | non_coding_transcript_exon_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.108 AC: 16420AN: 151932Hom.: 940 Cov.: 30
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GnomAD3 exomes AF: 0.106 AC: 26295AN: 248734Hom.: 1640 AF XY: 0.112 AC XY: 15049AN XY: 134386
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GnomAD4 exome AF: 0.115 AC: 166881AN: 1456094Hom.: 10115 Cov.: 30 AF XY: 0.117 AC XY: 84986AN XY: 724702
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GnomAD4 genome AF: 0.108 AC: 16425AN: 152048Hom.: 943 Cov.: 30 AF XY: 0.106 AC XY: 7886AN XY: 74318
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ClinVar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at