14-39040727-C-CTT
Position:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The ENST00000307712.11(SEC23A):c.2142+4_2142+5insAA variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00038 in 1,614,166 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0018 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00024 ( 1 hom. )
Consequence
SEC23A
ENST00000307712.11 splice_donor_region, intron
ENST00000307712.11 splice_donor_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.193
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP6
Variant 14-39040727-C-CTT is Benign according to our data. Variant chr14-39040727-C-CTT is described in ClinVar as [Likely_benign]. Clinvar id is 788183.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SEC23A | NM_006364.4 | c.2142+4_2142+5insAA | splice_donor_region_variant, intron_variant | ENST00000307712.11 | NP_006355.2 | |||
SEC23A | XM_005267262.2 | c.2214+4_2214+5insAA | splice_donor_region_variant, intron_variant | XP_005267319.1 | ||||
SEC23A | XM_011536355.4 | c.2214+4_2214+5insAA | splice_donor_region_variant, intron_variant | XP_011534657.1 | ||||
SEC23A | XM_017020928.3 | c.2142+4_2142+5insAA | splice_donor_region_variant, intron_variant | XP_016876417.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SEC23A | ENST00000307712.11 | c.2142+4_2142+5insAA | splice_donor_region_variant, intron_variant | 1 | NM_006364.4 | ENSP00000306881 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00177 AC: 270AN: 152204Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
270
AN:
152204
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000561 AC: 141AN: 251392Hom.: 0 AF XY: 0.000346 AC XY: 47AN XY: 135882
GnomAD3 exomes
AF:
AC:
141
AN:
251392
Hom.:
AF XY:
AC XY:
47
AN XY:
135882
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000235 AC: 344AN: 1461844Hom.: 1 Cov.: 30 AF XY: 0.000193 AC XY: 140AN XY: 727218
GnomAD4 exome
AF:
AC:
344
AN:
1461844
Hom.:
Cov.:
30
AF XY:
AC XY:
140
AN XY:
727218
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00177 AC: 270AN: 152322Hom.: 0 Cov.: 32 AF XY: 0.00170 AC XY: 127AN XY: 74490
GnomAD4 genome
AF:
AC:
270
AN:
152322
Hom.:
Cov.:
32
AF XY:
AC XY:
127
AN XY:
74490
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Craniolenticulosutural dysplasia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 04, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at