14-39040727-C-CTT

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

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.193
Variant links:
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 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
SEC23ANM_006364.4 linkuse as main transcriptc.2142+4_2142+5insAA splice_donor_region_variant, intron_variant ENST00000307712.11 NP_006355.2
SEC23AXM_005267262.2 linkuse as main transcriptc.2214+4_2214+5insAA splice_donor_region_variant, intron_variant XP_005267319.1
SEC23AXM_011536355.4 linkuse as main transcriptc.2214+4_2214+5insAA splice_donor_region_variant, intron_variant XP_011534657.1
SEC23AXM_017020928.3 linkuse as main transcriptc.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
SEC23AENST00000307712.11 linkuse as main transcriptc.2142+4_2142+5insAA splice_donor_region_variant, intron_variant 1 NM_006364.4 ENSP00000306881 P1Q15436-1

Frequencies

GnomAD3 genomes
AF:
0.00177
AC:
270
AN:
152204
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00591
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00118
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000441
Gnomad OTH
AF:
0.00191
GnomAD3 exomes
AF:
0.000561
AC:
141
AN:
251392
Hom.:
0
AF XY:
0.000346
AC XY:
47
AN XY:
135882
show subpopulations
Gnomad AFR exome
AF:
0.00646
Gnomad AMR exome
AF:
0.000838
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000352
Gnomad OTH exome
AF:
0.000489
GnomAD4 exome
AF:
0.000235
AC:
344
AN:
1461844
Hom.:
1
Cov.:
30
AF XY:
0.000193
AC XY:
140
AN XY:
727218
show subpopulations
Gnomad4 AFR exome
AF:
0.00657
Gnomad4 AMR exome
AF:
0.000850
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000459
Gnomad4 OTH exome
AF:
0.000563
GnomAD4 genome
AF:
0.00177
AC:
270
AN:
152322
Hom.:
0
Cov.:
32
AF XY:
0.00170
AC XY:
127
AN XY:
74490
show subpopulations
Gnomad4 AFR
AF:
0.00589
Gnomad4 AMR
AF:
0.00118
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000441
Gnomad4 OTH
AF:
0.00189
Alfa
AF:
0.000955
Hom.:
0
Bravo
AF:
0.00230

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 submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpAug 04, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs532535708; hg19: chr14-39509931; API