Genetic Variant SEC23A:c.2209-100_2209-99insTTATT (chr14-39033427-C-CAATAA) – 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.2209-100_2209-99insTTATT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0138 in 65,212 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.016 ( 3 hom., cov: 0)

Exomes 𝑓: 0.013 ( 2 hom. )

Consequence

SEC23A
NM_006364.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.184

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: MODERATE, SUPPORTIVE, LIMITED Submitted by: Orphanet, PanelApp Australia, 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 14-39033427-C-CAATAA is Benign according to our data. Variant chr14-39033427-C-CAATAA is described in ClinVar as Benign. ClinVar VariationId is 1252741.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006364.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SEC23A	NM_006364.4	MANE Select	c.2209-100_2209-99insTTATT		intron	N/A	NP_006355.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SEC23A	ENST00000307712.11	TSL:1 MANE Select	c.2209-100_2209-99insTTATT	intron	N/A	ENSP00000306881.6	Q15436-1
SEC23A	ENST00000554615.1	TSL:1	n.2404-100_2404-99insTTATT	intron	N/A
SEC23A	ENST00000857742.1		c.2281-100_2281-99insTTATT	intron	N/A	ENSP00000527801.1

Frequencies

GnomAD3 genomes

AF:

0.0161

AC:

222

AN:

13758

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0461

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00239

Gnomad ASJ

AF:

0.0136

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000193

Gnomad OTH

AF:

0.0116

GnomAD4 exome

AF:

0.0131

AC:

676

AN:

51436

Hom.:

AF XY:

0.0122

AC XY:

331

AN XY:

27232

show subpopulations

African (AFR)

AF:

0.183

AC:

371

AN:

2024

American (AMR)

AF:

0.0170

AC:

AN:

3004

Ashkenazi Jewish (ASJ)

AF:

0.0697

AC:

120

AN:

1722

East Asian (EAS)

AF:

0.00

AC:

AN:

1992

South Asian (SAS)

AF:

0.000341

AC:

AN:

5872

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3806

Middle Eastern (MID)

AF:

0.0225

AC:

AN:

222

European-Non Finnish (NFE)

AF:

0.00206

AC:

AN:

30168

Other (OTH)

AF:

0.0248

AC:

AN:

2626

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

115

154

192

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0161

AC:

222

AN:

13776

Hom.:

Cov.:

AF XY:

0.0159

AC XY:

110

AN XY:

6898

show subpopulations

African (AFR)

AF:

0.0461

AC:

211

AN:

4578

American (AMR)

AF:

0.00239

AC:

AN:

1672

Ashkenazi Jewish (ASJ)

AF:

0.0136

AC:

AN:

294

East Asian (EAS)

AF:

0.00

AC:

AN:

268

South Asian (SAS)

AF:

0.00

AC:

AN:

688

European-Finnish (FIN)

AF:

0.00

AC:

AN:

812

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.000193

AC:

AN:

5194

Other (OTH)

AF:

0.0110

AC:

AN:

182

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.18

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over