Variant chr20-18507755-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000336714.8(SEC23B):c.-250C>G 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 152,388 control chromosomes in the GnomAD database, including 53,630 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.83 ( 53599 hom., cov: 35)

Exomes 𝑓: 0.91 ( 31 hom. )

Consequence

SEC23B
ENST00000336714.8 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.0340

Variant links:

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]

SEC23B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BP6

Variant 20-18507755-C-G is Benign according to our data. Variant chr20-18507755-C-G is described in ClinVar as [Benign]. Clinvar id is 337781.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 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_032986.5 linkuse as main transcript	c.-15+86C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	Appris
SEC23B	ENST00000336714.8 linkuse as main transcript	c.-250C>G	5_prime_UTR_variant	1/20	1	P1
SEC23B	ENST00000262544.6 linkuse as main transcript	c.-290C>G	5_prime_UTR_variant	1/20	5	P1
SEC23B	ENST00000450074.6 linkuse as main transcript	c.-15+86C>G	intron_variant		5
SEC23B	ENST00000646240.1 linkuse as main transcript	c.-222+86C>G	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.830

AC:

126365

AN:

152194

Hom.:

53583

Cov.:

show subpopulations

Gnomad AFR

AF:

0.656

Gnomad AMI

AF:

0.979

Gnomad AMR

AF:

0.826

Gnomad ASJ

AF:

0.880

Gnomad EAS

AF:

0.728

Gnomad SAS

AF:

0.852

Gnomad FIN

AF:

0.901

Gnomad MID

AF:

0.873

Gnomad NFE

AF:

0.927

Gnomad OTH

AF:

0.847

GnomAD4 exome

AF:

0.908

AC:

AN:

Hom.:

Cov.:

AF XY:

0.929

AC XY:

AN XY:

show subpopulations

Gnomad4 AMR exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.750

Gnomad4 FIN exome

AF:

0.750

Gnomad4 NFE exome

AF:

0.929

Gnomad4 OTH exome

AF:

1.00

GnomAD4 genome

AF:

0.830

AC:

126431

AN:

152312

Hom.:

53599

Cov.:

AF XY:

0.829

AC XY:

61713

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.657

Gnomad4 AMR

AF:

0.826

Gnomad4 ASJ

AF:

0.880

Gnomad4 EAS

AF:

0.728

Gnomad4 SAS

AF:

0.853

Gnomad4 FIN

AF:

0.901

Gnomad4 NFE

AF:

0.927

Gnomad4 OTH

AF:

0.842

Alfa

AF:

0.866

Hom.:

2969

Bravo

AF:

0.813

Asia WGS

AF:

0.747

AC:

2597

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 27, 2018	- -

Congenital dyserythropoietic anemia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

3.3

DANN

Benign

0.48

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over