Genetic Variant SEC23A:c.2209-99_2209-98insTT (chr14-39033426-G-GAA) – 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.2209-99_2209-98insTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0149 in 60,114 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.019 ( 2 hom., cov: 0)

Exomes 𝑓: 0.014 ( 3 hom. )

Consequence

SEC23A
NM_006364.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.987

Publications

0 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:

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ACMG classification

Classification was made for transcript

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

BP6

Variant 14-39033426-G-GAA is Benign according to our data. Variant chr14-39033426-G-GAA is described in ClinVar as [Benign]. Clinvar id is 1280265.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEC23A	NM_006364.4 link	c.2209-99_2209-98insTT		intron_variant	Intron 19 of 19	ENST00000307712.11	NP_006355.2	Q15436-1
SEC23A	XM_005267262.2 link	c.2281-99_2281-98insTT		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.2209-99_2209-98insTT		intron_variant	Intron 19 of 19	1	NM_006364.4	ENSP00000306881.6		Q15436-1

Frequencies

GnomAD3 genomes

AF:

0.0186

AC:

220

AN:

11818

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0518

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00274

Gnomad ASJ

AF:

0.0149

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000231

Gnomad OTH

AF:

0.0149

GnomAD4 exome

AF:

0.0140

AC:

678

AN:

48278

Hom.:

AF XY:

0.0129

AC XY:

332

AN XY:

25650

show subpopulations

African (AFR)

AF:

0.190

AC:

372

AN:

1956

American (AMR)

AF:

0.0170

AC:

AN:

2992

Ashkenazi Jewish (ASJ)

AF:

0.0742

AC:

120

AN:

1618

East Asian (EAS)

AF:

0.00

AC:

AN:

1772

South Asian (SAS)

AF:

0.000345

AC:

AN:

5802

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3454

Middle Eastern (MID)

AF:

0.0248

AC:

AN:

202

European-Non Finnish (NFE)

AF:

0.00225

AC:

AN:

28002

Other (OTH)

AF:

0.0262

AC:

AN:

2480

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

113

150

188

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0186

AC:

220

AN:

11836

Hom.:

Cov.:

AF XY:

0.0182

AC XY:

108

AN XY:

5942

show subpopulations

African (AFR)

AF:

0.0518

AC:

209

AN:

4034

American (AMR)

AF:

0.00274

AC:

AN:

1460

Ashkenazi Jewish (ASJ)

AF:

0.0149

AC:

AN:

268

East Asian (EAS)

AF:

0.00

AC:

AN:

224

South Asian (SAS)

AF:

0.00

AC:

AN:

628

European-Finnish (FIN)

AF:

0.00

AC:

AN:

668

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.000231

AC:

AN:

4336

Other (OTH)

AF:

0.0139

AC:

AN:

144

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

May 23, 2021

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

-0.99

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Publications

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chr14-39033426-G-GAA

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