Genetic Variant SEC23A:c.2209-95_2209-94insGTTCTATT (chr14-39033422-A-AAATAGAAC) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_006364.4(SEC23A):c.2209-95_2209-94insGTTCTATT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.918 in 755,254 control chromosomes in the GnomAD database, including 319,834 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.80 ( 9193 hom., cov: 0)

Exomes 𝑓: 0.92 ( 310641 hom. )

Consequence

SEC23A
NM_006364.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.00

Publications

1 publications found

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 Gene-Disease associations (from GenCC):

craniolenticulosutural dysplasia
Inheritance: AR, Unknown Classification: SUPPORTIVE, LIMITED Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P

SEC23A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 14-39033422-A-AAATAGAAC is Benign according to our data. Variant chr14-39033422-A-AAATAGAAC is described in ClinVar as [Benign]. Clinvar id is 1283041.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEC23A	NM_006364.4 link	c.2209-95_2209-94insGTTCTATT		intron_variant	Intron 19 of 19	ENST00000307712.11	NP_006355.2	Q15436-1
SEC23A	XM_005267262.2 link	c.2281-95_2281-94insGTTCTATT		intron_variant	Intron 20 of 20		XP_005267319.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEC23A	ENST00000307712.11 link	c.2209-95_2209-94insGTTCTATT		intron_variant	Intron 19 of 19	1	NM_006364.4	ENSP00000306881.6		Q15436-1

Frequencies

GnomAD3 genomes

AF:

0.804

AC:

22892

AN:

28458

Hom.:

9181

Cov.:

show subpopulations

Gnomad AFR

AF:

0.836

Gnomad AMI

AF:

0.897

Gnomad AMR

AF:

0.699

Gnomad ASJ

AF:

0.723

Gnomad EAS

AF:

0.901

Gnomad SAS

AF:

0.674

Gnomad FIN

AF:

0.814

Gnomad MID

AF:

0.625

Gnomad NFE

AF:

0.816

Gnomad OTH

AF:

0.810

GnomAD4 exome

AF:

0.922

AC:

670289

AN:

726744

Hom.:

310641

AF XY:

0.919

AC XY:

355151

AN XY:

386488

show subpopulations

African (AFR)

AF:

0.908

AC:

17270

AN:

19030

American (AMR)

AF:

0.847

AC:

32912

AN:

38858

Ashkenazi Jewish (ASJ)

AF:

0.913

AC:

18954

AN:

20762

East Asian (EAS)

AF:

0.976

AC:

35199

AN:

36070

South Asian (SAS)

AF:

0.837

AC:

57264

AN:

68424

European-Finnish (FIN)

AF:

0.921

AC:

47610

AN:

51668

Middle Eastern (MID)

AF:

0.914

AC:

2516

AN:

2754

European-Non Finnish (NFE)

AF:

0.939

AC:

425449

AN:

453236

Other (OTH)

AF:

0.921

AC:

33115

AN:

35942

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

2318

4636

6953

9271

11589

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.804

AC:

22926

AN:

28510

Hom.:

9193

Cov.:

AF XY:

0.798

AC XY:

11802

AN XY:

14794

show subpopulations

African (AFR)

AF:

0.836

AC:

8876

AN:

10618

American (AMR)

AF:

0.698

AC:

2129

AN:

3052

Ashkenazi Jewish (ASJ)

AF:

0.723

AC:

337

AN:

466

East Asian (EAS)

AF:

0.899

AC:

620

AN:

690

South Asian (SAS)

AF:

0.673

AC:

898

AN:

1334

European-Finnish (FIN)

AF:

0.814

AC:

1469

AN:

1804

Middle Eastern (MID)

AF:

0.620

AC:

AN:

European-Non Finnish (NFE)

AF:

0.816

AC:

8171

AN:

10012

Other (OTH)

AF:

0.800

AC:

325

AN:

406

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

222

444

665

887

1109

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.924

Hom.:

5063

Bravo

AF:

0.924

Asia WGS

AF:

0.664

AC:

1015

AN:

1524

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jul 27, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

3.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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chr14-39033422-A-AAATAGAAC

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over