Variant 10-73760307-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_198597.3(SEC24C):c.771C>G(p.Gly257Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00889 in 1,613,340 control chromosomes in the GnomAD database, including 94 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0072 ( 9 hom., cov: 32)

Exomes 𝑓: 0.0091 ( 85 hom. )

Consequence

SEC24C
NM_198597.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0800

Variant links:

Genes affected

SEC24C (HGNC:10705): (SEC24 homolog C, COPII coat complex component) The protein encoded by this gene is a member of the SEC24 subfamily of the SEC23/SEC24 family, which is involved in vesicle trafficking. The encoded protein has similarity to yeast Sec24p component of COPII. COPII is the coat protein complex responsible for vesicle budding from the ER. The product of this gene may play a role in shaping the vesicle, as well as in cargo selection and concentration. Alternatively spliced transcript variants encoding the same protein have been identified. [provided by RefSeq, Jul 2008]

SEC24C links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 10-73760307-C-G is Benign according to our data. Variant chr10-73760307-C-G is described in ClinVar as [Benign]. Clinvar id is 771741.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.08 with no splicing effect.

BS2

High AC in GnomAd4 at 1103 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SEC24C	NM_198597.3 linkuse as main transcript	c.771C>G	p.Gly257Gly	synonymous_variant	5/23	ENST00000345254.9	NP_940999.1	P53992-1A0A024QZM6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SEC24C	ENST00000345254.9 linkuse as main transcript	c.771C>G	p.Gly257Gly	synonymous_variant	5/23	1	NM_198597.3	ENSP00000321845.6		P53992-1

Frequencies

GnomAD3 genomes

AF:

0.00725

AC:

1103

AN:

152168

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00282

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00517

Gnomad ASJ

AF:

0.0239

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00580

Gnomad FIN

AF:

0.00471

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0105

Gnomad OTH

AF:

0.0120

GnomAD3 exomes

AF:

0.00758

AC:

1900

AN:

250530

Hom.:

AF XY:

0.00823

AC XY:

1115

AN XY:

135470

show subpopulations

Gnomad AFR exome

AF:

0.00259

Gnomad AMR exome

AF:

0.00471

Gnomad ASJ exome

AF:

0.0162

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00882

Gnomad FIN exome

AF:

0.00505

Gnomad NFE exome

AF:

0.00970

Gnomad OTH exome

AF:

0.00866

GnomAD4 exome

AF:

0.00906

AC:

13236

AN:

1461054

Hom.:

Cov.:

AF XY:

0.00933

AC XY:

6779

AN XY:

726882

show subpopulations

Gnomad4 AFR exome

AF:

0.00251

Gnomad4 AMR exome

AF:

0.00561

Gnomad4 ASJ exome

AF:

0.0162

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00926

Gnomad4 FIN exome

AF:

0.00524

Gnomad4 NFE exome

AF:

0.00973

Gnomad4 OTH exome

AF:

0.00866

GnomAD4 genome

AF:

0.00724

AC:

1103

AN:

152286

Hom.:

Cov.:

AF XY:

0.00713

AC XY:

531

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.00282

Gnomad4 AMR

AF:

0.00516

Gnomad4 ASJ

AF:

0.0239

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00622

Gnomad4 FIN

AF:

0.00471

Gnomad4 NFE

AF:

0.0105

Gnomad4 OTH

AF:

0.0118

Alfa

AF:

0.00738

Hom.:

Bravo

AF:

0.00683

Asia WGS

AF:

0.00491

AC:

AN:

3478

EpiCase

AF:

0.0123

EpiControl

AF:

0.0114

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

5.6

DANN

Benign

0.60

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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