Variant 3-10301303-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_183352.3(SEC13):c.927C>T(p.Ser309=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00411 in 1,614,120 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0027 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0043 ( 24 hom. )

Consequence

SEC13
NM_183352.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.44

Variant links:

Genes affected

SEC13 (HGNC:10697): (SEC13 homolog, nuclear pore and COPII coat complex component) The protein encoded by this gene belongs to the SEC13 family of WD-repeat proteins. It is a constituent of the endoplasmic reticulum and the nuclear pore complex. It has similarity to the yeast SEC13 protein, which is required for vesicle biogenesis from endoplasmic reticulum during the transport of proteins. Multiple alternatively spliced transcript variants have been found. [provided by RefSeq, Oct 2008]

SEC13 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.34).

BP6

Variant 3-10301303-G-A is Benign according to our data. Variant chr3-10301303-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2653520.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.44 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SEC13	NM_183352.3 linkuse as main transcript	c.927C>T	p.Ser309=	synonymous_variant	9/9	ENST00000350697.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SEC13	ENST00000350697.8 linkuse as main transcript	c.927C>T	p.Ser309=	synonymous_variant	9/9	1	NM_183352.3	P4	P55735-1

Frequencies

GnomAD3 genomes

AF:

0.00273

AC:

416

AN:

152118

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000821

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.00425

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.000471

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00440

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00273

AC:

687

AN:

251450

Hom.:

AF XY:

0.00266

AC XY:

361

AN XY:

135900

show subpopulations

Gnomad AFR exome

AF:

0.00105

Gnomad AMR exome

AF:

0.00260

Gnomad ASJ exome

AF:

0.000595

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00121

Gnomad FIN exome

AF:

0.000416

Gnomad NFE exome

AF:

0.00455

Gnomad OTH exome

AF:

0.00163

GnomAD4 exome

AF:

0.00425

AC:

6213

AN:

1461884

Hom.:

Cov.:

AF XY:

0.00421

AC XY:

3060

AN XY:

727248

show subpopulations

Gnomad4 AFR exome

AF:

0.000777

Gnomad4 AMR exome

AF:

0.00255

Gnomad4 ASJ exome

AF:

0.000957

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.00103

Gnomad4 FIN exome

AF:

0.000580

Gnomad4 NFE exome

AF:

0.00517

Gnomad4 OTH exome

AF:

0.00272

GnomAD4 genome

AF:

0.00273

AC:

416

AN:

152236

Hom.:

Cov.:

AF XY:

0.00271

AC XY:

202

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.000818

Gnomad4 AMR

AF:

0.00425

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00125

Gnomad4 FIN

AF:

0.000471

Gnomad4 NFE

AF:

0.00440

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00372

Hom.:

Bravo

AF:

0.00320

EpiCase

AF:

0.00376

EpiControl

AF:

0.00385

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2023

SEC13: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.34

CADD

Benign

5.2

DANN

Benign

0.68

RBP_binding_hub_radar

0.97

RBP_regulation_power_radar

2.7

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