14-39033422-A-AAATAGAAC

Position:

• chr14-39033422-A-AAATAGAAC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.00

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SEC23A	NM_006364.4	c.2209-95_2209-94insGTTCTATT		intron_variant		ENST00000307712.11	NP_006355.2
SEC23A	XM_005267262.2	c.2281-95_2281-94insGTTCTATT		intron_variant			XP_005267319.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SEC23A	ENST00000307712.11	c.2209-95_2209-94insGTTCTATT		intron_variant		1	NM_006364.4	ENSP00000306881	P1

Frequencies

GnomAD3 genomes AF: 0.804 AC: 22892 AN: 28458 Hom.: 9181 Cov.: 0

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

Gnomad4 AFR exome AF: 0.908

Gnomad4 AMR exome AF: 0.847

Gnomad4 ASJ exome AF: 0.913

Gnomad4 EAS exome AF: 0.976

Gnomad4 SAS exome AF: 0.837

Gnomad4 FIN exome AF: 0.921

Gnomad4 NFE exome AF: 0.939

Gnomad4 OTH exome AF: 0.921

GnomAD4 genome AF: 0.804 AC: 22926 AN: 28510 Hom.: 9193 Cov.: 0 AF XY: 0.798 AC XY: 11802 AN XY: 14794

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.723

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.673

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.800

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

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 27, 2018

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11283010; hg19: chr14-39502626;