Variant 14-39042748-CT-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_006364.4(SEC23A):c.1986+37del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 1,317,144 control chromosomes in the GnomAD database, including 42,253 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.21 ( 3842 hom., cov: 27)

Exomes 𝑓: 0.25 ( 38411 hom. )

Consequence

SEC23A
NM_006364.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.46

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 -10 ACMG points.

BP6

Variant 14-39042748-CT-C is Benign according to our data. Variant chr14-39042748-CT-C is described in ClinVar as [Benign]. Clinvar id is 1242001.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
SEC23A	NM_006364.4 linkuse as main transcript	c.1986+37del	intron_variant	ENST00000307712.11	NP_006355.2
SEC23A	XM_005267262.2 linkuse as main transcript	c.2058+37del	intron_variant		XP_005267319.1
SEC23A	XM_011536355.4 linkuse as main transcript	c.2058+37del	intron_variant		XP_011534657.1
SEC23A	XM_017020928.3 linkuse as main transcript	c.1986+37del	intron_variant		XP_016876417.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
SEC23A	ENST00000307712.11 linkuse as main transcript	c.1986+37del	intron_variant	1	NM_006364.4	ENSP00000306881	P1	Q15436-1
SEC23A	ENST00000537403.5 linkuse as main transcript	c.1380+37del	intron_variant	2		ENSP00000444193		Q15436-2
SEC23A	ENST00000545328.6 linkuse as main transcript	c.1899+37del	intron_variant	2		ENSP00000445393

Frequencies

GnomAD3 genomes

AF:

0.209

AC:

31748

AN:

151916

Hom.:

3849

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0858

Gnomad AMI

AF:

0.279

Gnomad AMR

AF:

0.220

Gnomad ASJ

AF:

0.382

Gnomad EAS

AF:

0.246

Gnomad SAS

AF:

0.288

Gnomad FIN

AF:

0.241

Gnomad MID

AF:

0.345

Gnomad NFE

AF:

0.256

Gnomad OTH

AF:

0.258

GnomAD3 exomes

AF:

0.250

AC:

62410

AN:

249634

Hom.:

8460

AF XY:

0.260

AC XY:

35057

AN XY:

134942

show subpopulations

Gnomad AFR exome

AF:

0.0810

Gnomad AMR exome

AF:

0.198

Gnomad ASJ exome

AF:

0.400

Gnomad EAS exome

AF:

0.262

Gnomad SAS exome

AF:

0.296

Gnomad FIN exome

AF:

0.242

Gnomad NFE exome

AF:

0.262

Gnomad OTH exome

AF:

0.278

GnomAD4 exome

AF:

0.252

AC:

293274

AN:

1165108

Hom.:

38411

Cov.:

AF XY:

0.256

AC XY:

152203

AN XY:

595080

show subpopulations

Gnomad4 AFR exome

AF:

0.0818

Gnomad4 AMR exome

AF:

0.200

Gnomad4 ASJ exome

AF:

0.393

Gnomad4 EAS exome

AF:

0.233

Gnomad4 SAS exome

AF:

0.296

Gnomad4 FIN exome

AF:

0.249

Gnomad4 NFE exome

AF:

0.252

Gnomad4 OTH exome

AF:

0.258

GnomAD4 genome

AF:

0.209

AC:

31729

AN:

152036

Hom.:

3842

Cov.:

AF XY:

0.210

AC XY:

15625

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.0857

Gnomad4 AMR

AF:

0.219

Gnomad4 ASJ

AF:

0.382

Gnomad4 EAS

AF:

0.244

Gnomad4 SAS

AF:

0.289

Gnomad4 FIN

AF:

0.241

Gnomad4 NFE

AF:

0.256

Gnomad4 OTH

AF:

0.255

Alfa

AF:

0.254

Hom.:

1031

Bravo

AF:

0.202

Asia WGS

AF:

0.206

AC:

717

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 05, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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