chr14-39033335-G-GA
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_006364.4(SEC23A):c.2209-8_2209-7insT variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.923 in 1,411,282 control chromosomes in the GnomAD database, including 602,938 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.81 ( 9419 hom., cov: 0)
Exomes 𝑓: 0.93 ( 593519 hom. )
Consequence
SEC23A
NM_006364.4 splice_region, splice_polypyrimidine_tract, intron
NM_006364.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.13
Genes affected
SEC23A (HGNC:10701): (SEC23 homolog A, COPII coat complex component) The protein encoded by this gene is a member of the SEC23 subfamily of the SEC23/SEC24 family. It is part of a protein complex and found in the ribosome-free transitional face of the endoplasmic reticulum (ER) and associated vesicles. This protein has similarity to yeast Sec23p component of COPII. COPII is the coat protein complex responsible for vesicle budding from the ER. The encoded protein is suggested to play a role in the ER-Golgi protein trafficking. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
?
Variant 14-39033335-G-GA is Benign according to our data. Variant chr14-39033335-G-GA is described in ClinVar as [Benign]. Clinvar id is 683759.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
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GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEC23A | NM_006364.4 | c.2209-8_2209-7insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000307712.11 | |||
SEC23A | XM_005267262.2 | c.2281-8_2281-7insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEC23A | ENST00000307712.11 | c.2209-8_2209-7insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_006364.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.811 AC: 23203AN: 28614Hom.: 9411 Cov.: 0
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GnomAD3 exomes AF: 0.915 AC: 229645AN: 251066Hom.: 105285 AF XY: 0.913 AC XY: 123951AN XY: 135760
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GnomAD4 exome AF: 0.925 AC: 1279453AN: 1382620Hom.: 593519 Cov.: 24 AF XY: 0.924 AC XY: 640201AN XY: 693010
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GnomAD4 genome ? AF: 0.811 AC: 23231AN: 28662Hom.: 9419 Cov.: 0 AF XY: 0.804 AC XY: 11958AN XY: 14868
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Craniolenticulosutural dysplasia Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 14, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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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