chr20-18508110-G-C

Position:

• chr20-18508110-G-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000377465.6(SEC23B):​c.-202G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.83 in 152,188 control chromosomes in the GnomAD database, including 53,587 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.83 (53564 hom., cov: 31)
  • Exomes 𝑓: 0.91 (23 hom.)
• Consequence: SEC23B ENST00000377465.6 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.71

Genes affected

SEC23B (HGNC:10702): (SEC23 homolog B, COPII coat complex component) The protein encoded by this gene is a member of the SEC23 subfamily of the SEC23/SEC24 family, which is involved in vesicle trafficking. The encoded protein has similarity to yeast Sec23p component of COPII. COPII is the coat protein complex responsible for vesicle budding from the ER. The function of this gene product has been implicated in cargo selection and concentration. Multiple alternatively spliced transcript variants have been identified in this gene. [provided by RefSeq, Feb 2010]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BP6: Variant 20-18508110-G-C is Benign according to our data. Variant chr20-18508110-G-C is described in ClinVar as [Benign]. Clinvar id is 1281680.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SEC23B	NM_006363.6	c.-15+138G>C		intron_variant		ENST00000650089.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SEC23B	ENST00000650089.1	c.-15+138G>C		intron_variant			NM_006363.6	P1

Frequencies

GnomAD3 genomes AF: 0.831 AC: 126257 AN: 152016 Hom.: 53548 Cov.: 31

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.979

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.901

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.927

Gnomad OTH AF: 0.847

GnomAD4 exome AF: 0.907 AC: 49 AN: 54 Hom.: 23 Cov.: 0 AF XY: 0.913 AC XY: 42 AN XY: 46

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.957

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.830 AC: 126323 AN: 152134 Hom.: 53564 Cov.: 31 AF XY: 0.829 AC XY: 61636 AN XY: 74362

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.826

Gnomad4 ASJ AF: 0.880

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.853

Gnomad4 FIN AF: 0.901

Gnomad4 NFE AF: 0.927

Gnomad4 OTH AF: 0.842

Alfa AF: 0.865 Hom.: 3372

Bravo AF: 0.813

Asia WGS AF: 0.747 AC: 2595 AN: 3478

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

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.48
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2281576; hg19: chr20-18488754;