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GeneBe

14-39042878-G-A

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_006364.4(SEC23A):c.1900-6C>T 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 0.000034 in 1,587,078 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00018 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000019 ( 0 hom. )

Consequence

SEC23A
NM_006364.4 splice_region, splice_polypyrimidine_tract, intron

Scores

2
Splicing: ADA: 0.00002824
2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.211
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 -6 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 14-39042878-G-A is Benign according to our data. Variant chr14-39042878-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2715411.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SEC23ANM_006364.4 linkuse as main transcriptc.1900-6C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant ENST00000307712.11
SEC23AXM_005267262.2 linkuse as main transcriptc.1972-6C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant
SEC23AXM_011536355.4 linkuse as main transcriptc.1972-6C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant
SEC23AXM_017020928.3 linkuse as main transcriptc.1900-6C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SEC23AENST00000307712.11 linkuse as main transcriptc.1900-6C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 1 NM_006364.4 P1Q15436-1
SEC23AENST00000537403.5 linkuse as main transcriptc.1294-6C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 2 Q15436-2
SEC23AENST00000545328.6 linkuse as main transcriptc.1813-6C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.000178
AC:
27
AN:
151738
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000485
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00164
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:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000398
AC:
10
AN:
251320
Hom.:
0
AF XY:
0.0000368
AC XY:
5
AN XY:
135852
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000145
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000176
Gnomad OTH exome
AF:
0.000163
GnomAD4 exome
AF:
0.0000188
AC:
27
AN:
1435218
Hom.:
0
Cov.:
27
AF XY:
0.0000182
AC XY:
13
AN XY:
715756
show subpopulations
Gnomad4 AFR exome
AF:
0.0000304
Gnomad4 AMR exome
AF:
0.000291
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000255
Gnomad4 SAS exome
AF:
0.0000234
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000551
Gnomad4 OTH exome
AF:
0.0000673
GnomAD4 genome
AF:
0.000178
AC:
27
AN:
151860
Hom.:
0
Cov.:
33
AF XY:
0.000216
AC XY:
16
AN XY:
74230
show subpopulations
Gnomad4 AFR
AF:
0.0000484
Gnomad4 AMR
AF:
0.00164
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.000332
EpiCase
AF:
0.0000547
EpiControl
AF:
0.00

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 testingInvitaeSep 28, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
Cadd
Benign
0.13
Dann
Benign
0.42

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.000028
dbscSNV1_RF
Benign
0.0020
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs201330860; hg19: chr14-39512082; API