14-39033427-C-CAATAA

Position:

• chr14-39033427-C-CAATAA

Variant summary

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

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.184

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 14-39033427-C-CAATAA is Benign according to our data. Variant chr14-39033427-C-CAATAA is described in ClinVar as [Benign]. Clinvar id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SEC23A	NM_006364.4	c.2209-100_2209-99insTTATT		intron_variant		ENST00000307712.11	NP_006355.2
SEC23A	XM_005267262.2	c.2281-100_2281-99insTTATT		intron_variant			XP_005267319.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SEC23A	ENST00000307712.11	c.2209-100_2209-99insTTATT		intron_variant		1	NM_006364.4	ENSP00000306881	P1

Frequencies

GnomAD3 genomes AF: 0.0161 AC: 222 AN: 13758 Hom.: 3 Cov.: 0

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.: 2 AF XY: 0.0122 AC XY: 331 AN XY: 27232

Gnomad4 AFR exome AF: 0.183

Gnomad4 AMR exome AF: 0.0170

Gnomad4 ASJ exome AF: 0.0697

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000341

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00206

Gnomad4 OTH exome AF: 0.0248

GnomAD4 genome AF: 0.0161 AC: 222 AN: 13776 Hom.: 3 Cov.: 0 AF XY: 0.0159 AC XY: 110 AN XY: 6898

Gnomad4 AFR AF: 0.0461

Gnomad4 AMR AF: 0.00239

Gnomad4 ASJ AF: 0.0136

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000193

Gnomad4 OTH AF: 0.0110

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

May 23, 2021

- -

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: rs528496953; hg19: chr14-39502631;