chr10-119898593-A-G
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_007190.4(SEC23IP):āc.330A>Gā(p.Gln110=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00246 in 1,614,202 control chromosomes in the GnomAD database, including 88 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.013 ( 38 hom., cov: 32)
Exomes š: 0.0014 ( 50 hom. )
Consequence
SEC23IP
NM_007190.4 synonymous
NM_007190.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.979
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=-0.95).
BP6
Variant 10-119898593-A-G is Benign according to our data. Variant chr10-119898593-A-G is described in ClinVar as [Benign]. Clinvar id is 782536.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.979 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.013 (1980/152318) while in subpopulation AFR AF= 0.0452 (1878/41564). AF 95% confidence interval is 0.0435. There are 38 homozygotes in gnomad4. There are 900 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 38 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEC23IP | NM_007190.4 | c.330A>G | p.Gln110= | synonymous_variant | 2/19 | ENST00000369075.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEC23IP | ENST00000369075.8 | c.330A>G | p.Gln110= | synonymous_variant | 2/19 | 1 | NM_007190.4 | P4 | |
SEC23IP | ENST00000705471.1 | c.330A>G | p.Gln110= | synonymous_variant | 2/19 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0129 AC: 1970AN: 152200Hom.: 38 Cov.: 32
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GnomAD3 exomes AF: 0.00348 AC: 875AN: 251482Hom.: 21 AF XY: 0.00246 AC XY: 334AN XY: 135918
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GnomAD4 exome AF: 0.00136 AC: 1992AN: 1461884Hom.: 50 Cov.: 32 AF XY: 0.00117 AC XY: 850AN XY: 727242
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GnomAD4 genome AF: 0.0130 AC: 1980AN: 152318Hom.: 38 Cov.: 32 AF XY: 0.0121 AC XY: 900AN XY: 74496
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 20, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at