10-119920847-A-G
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_007190.4(SEC23IP):c.2026-42A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0702 in 1,295,424 control chromosomes in the GnomAD database, including 5,537 homozygotes. 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 0.055 ( 430 hom., cov: 33)
Exomes 𝑓: 0.072 ( 5107 hom. )
Consequence
SEC23IP
NM_007190.4 intron
NM_007190.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.90
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 -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SEC23IP | ENST00000369075.8 | c.2026-42A>G | intron_variant | Intron 11 of 18 | 1 | NM_007190.4 | ENSP00000358071.3 | |||
SEC23IP | ENST00000705471.1 | c.2026-42A>G | intron_variant | Intron 11 of 18 | ENSP00000516127.1 |
Frequencies
GnomAD3 genomes AF: 0.0547 AC: 8330AN: 152196Hom.: 430 Cov.: 33
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GnomAD3 exomes AF: 0.0880 AC: 20105AN: 228366Hom.: 1542 AF XY: 0.0959 AC XY: 11847AN XY: 123498
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GnomAD4 exome AF: 0.0723 AC: 82639AN: 1143110Hom.: 5107 Cov.: 14 AF XY: 0.0784 AC XY: 45560AN XY: 581382
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GnomAD4 genome AF: 0.0547 AC: 8336AN: 152314Hom.: 430 Cov.: 33 AF XY: 0.0601 AC XY: 4476AN XY: 74488
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at