rs17108797
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_006364.4(SEC23A):āc.927T>Cā(p.Pro309=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0589 in 1,613,692 control chromosomes in the GnomAD database, including 3,273 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.047 ( 244 hom., cov: 32)
Exomes š: 0.060 ( 3029 hom. )
Consequence
SEC23A
NM_006364.4 synonymous
NM_006364.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0660
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 -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
?
Variant 14-39075995-A-G is Benign according to our data. Variant chr14-39075995-A-G is described in ClinVar as [Benign]. Clinvar id is 464900.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.066 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0621 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEC23A | NM_006364.4 | c.927T>C | p.Pro309= | synonymous_variant | 8/20 | ENST00000307712.11 | |
SEC23A | XM_005267262.2 | c.927T>C | p.Pro309= | synonymous_variant | 8/21 | ||
SEC23A | XM_011536355.4 | c.927T>C | p.Pro309= | synonymous_variant | 8/21 | ||
SEC23A | XM_017020928.3 | c.927T>C | p.Pro309= | synonymous_variant | 8/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEC23A | ENST00000307712.11 | c.927T>C | p.Pro309= | synonymous_variant | 8/20 | 1 | NM_006364.4 | P1 | |
SEC23A | ENST00000545328.6 | c.840T>C | p.Pro280= | synonymous_variant | 7/19 | 2 | |||
SEC23A | ENST00000537403.5 | c.321T>C | p.Pro107= | synonymous_variant | 4/16 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0472 AC: 7174AN: 152138Hom.: 245 Cov.: 32
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GnomAD3 exomes AF: 0.0509 AC: 12795AN: 251296Hom.: 443 AF XY: 0.0527 AC XY: 7154AN XY: 135830
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GnomAD4 exome AF: 0.0601 AC: 87860AN: 1461436Hom.: 3029 Cov.: 32 AF XY: 0.0599 AC XY: 43526AN XY: 727038
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GnomAD4 genome ? AF: 0.0471 AC: 7168AN: 152256Hom.: 244 Cov.: 32 AF XY: 0.0469 AC XY: 3491AN XY: 74452
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
SEC23A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 15, 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). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 16, 2018 | - - |
Craniolenticulosutural dysplasia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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