rs34826964
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_007190.4(SEC23IP):āc.2970A>Gā(p.Thr990=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0675 in 1,594,410 control chromosomes in the GnomAD database, including 6,289 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.055 ( 432 hom., cov: 33)
Exomes š: 0.069 ( 5857 hom. )
Consequence
SEC23IP
NM_007190.4 synonymous
NM_007190.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.549
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
?
Variant 10-119933734-A-G is Benign according to our data. Variant chr10-119933734-A-G is described in ClinVar as [Benign]. Clinvar id is 3056457.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.549 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEC23IP | NM_007190.4 | c.2970A>G | p.Thr990= | synonymous_variant | 18/19 | ENST00000369075.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEC23IP | ENST00000369075.8 | c.2970A>G | p.Thr990= | synonymous_variant | 18/19 | 1 | NM_007190.4 | P4 | |
SEC23IP | ENST00000705471.1 | c.2967A>G | p.Thr989= | synonymous_variant | 18/19 | A1 | |||
SEC23IP | ENST00000475542.1 | n.516A>G | non_coding_transcript_exon_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0547 AC: 8330AN: 152168Hom.: 432 Cov.: 33
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GnomAD3 exomes AF: 0.0885 AC: 22192AN: 250620Hom.: 1713 AF XY: 0.0973 AC XY: 13187AN XY: 135514
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GnomAD4 exome AF: 0.0688 AC: 99230AN: 1442124Hom.: 5857 Cov.: 27 AF XY: 0.0748 AC XY: 53775AN XY: 718684
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GnomAD4 genome ? AF: 0.0547 AC: 8335AN: 152286Hom.: 432 Cov.: 33 AF XY: 0.0601 AC XY: 4473AN XY: 74448
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SEC23IP-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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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