Variant chr14-39039403-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006364.4(SEC23A):c.2143-307G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 283,456 control chromosomes in the GnomAD database, including 3,508 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 1944 hom., cov: 32)

Exomes 𝑓: 0.15 ( 1564 hom. )

Consequence

SEC23A
NM_006364.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.56

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]

SEC23A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 14-39039403-C-T is Benign according to our data. Variant chr14-39039403-C-T is described in ClinVar as [Benign]. Clinvar id is 1181688.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
SEC23A	NM_006364.4 linkuse as main transcript	c.2143-307G>A	intron_variant	ENST00000307712.11	NP_006355.2
SEC23A	XM_005267262.2 linkuse as main transcript	c.2215-307G>A	intron_variant		XP_005267319.1
SEC23A	XM_011536355.4 linkuse as main transcript	c.2215-307G>A	intron_variant		XP_011534657.1
SEC23A	XM_017020928.3 linkuse as main transcript	c.2143-307G>A	intron_variant		XP_016876417.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SEC23A	ENST00000307712.11 linkuse as main transcript	c.2143-307G>A		intron_variant		1	NM_006364.4	ENSP00000306881	P1	Q15436-1

Frequencies

GnomAD3 genomes

AF:

0.157

AC:

23824

AN:

151636

Hom.:

1947

Cov.:

show subpopulations

Gnomad AFR

AF:

0.169

Gnomad AMI

AF:

0.214

Gnomad AMR

AF:

0.187

Gnomad ASJ

AF:

0.152

Gnomad EAS

AF:

0.175

Gnomad SAS

AF:

0.147

Gnomad FIN

AF:

0.155

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.142

Gnomad OTH

AF:

0.158

GnomAD4 exome

AF:

0.147

AC:

19341

AN:

131704

Hom.:

1564

Cov.:

AF XY:

0.147

AC XY:

10189

AN XY:

69500

show subpopulations

Gnomad4 AFR exome

AF:

0.217

Gnomad4 AMR exome

AF:

0.202

Gnomad4 ASJ exome

AF:

0.147

Gnomad4 EAS exome

AF:

0.174

Gnomad4 SAS exome

AF:

0.140

Gnomad4 FIN exome

AF:

0.147

Gnomad4 NFE exome

AF:

0.139

Gnomad4 OTH exome

AF:

0.154

GnomAD4 genome

AF:

0.157

AC:

23833

AN:

151752

Hom.:

1944

Cov.:

AF XY:

0.158

AC XY:

11691

AN XY:

74178

show subpopulations

Gnomad4 AFR

AF:

0.169

Gnomad4 AMR

AF:

0.187

Gnomad4 ASJ

AF:

0.152

Gnomad4 EAS

AF:

0.175

Gnomad4 SAS

AF:

0.147

Gnomad4 FIN

AF:

0.155

Gnomad4 NFE

AF:

0.142

Gnomad4 OTH

AF:

0.157

Alfa

AF:

0.144

Hom.:

177

Bravo

AF:

0.161

Asia WGS

AF:

0.160

AC:

555

AN:

3472

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 27, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.10

DANN

Benign

0.28

Splicing

Name

Calibrated prediction

Score

Prediction

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over