dbSNP rs11541237: SEC24C:n.*502C>T (chr10-73771204-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000465076.5(SEC24C):n.*502C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 1,307,972 control chromosomes in the GnomAD database, including 13,379 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.14 ( 1488 hom., cov: 32)

Exomes 𝑓: 0.14 ( 11891 hom. )

Consequence

SEC24C
ENST00000465076.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.651

Publications

13 publications found

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 Gene-Disease associations (from GenCC):

22q11.2 deletion syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

SEC24C links:

ENSG00000279689 (HGNC:):

ENSG00000279689 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.41).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEC24C	NM_198597.3 link	c.*109C>T		3_prime_UTR_variant	Exon 23 of 23	ENST00000345254.9	NP_940999.1	P53992-1A0A024QZM6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEC24C	ENST00000345254.9 link	c.*109C>T		3_prime_UTR_variant	Exon 23 of 23	1	NM_198597.3	ENSP00000321845.6		P53992-1

Frequencies

GnomAD3 genomes

AF:

0.137

AC:

20784

AN:

151956

Hom.:

1470

Cov.:

show subpopulations

Gnomad AFR

AF:

0.139

Gnomad AMI

AF:

0.175

Gnomad AMR

AF:

0.106

Gnomad ASJ

AF:

0.229

Gnomad EAS

AF:

0.123

Gnomad SAS

AF:

0.195

Gnomad FIN

AF:

0.133

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.135

Gnomad OTH

AF:

0.131

GnomAD4 exome

AF:

0.140

AC:

161433

AN:

1155898

Hom.:

11891

Cov.:

AF XY:

0.142

AC XY:

82207

AN XY:

577752

show subpopulations

African (AFR)

AF:

0.140

AC:

3674

AN:

26188

American (AMR)

AF:

0.0918

AC:

2758

AN:

30046

Ashkenazi Jewish (ASJ)

AF:

0.230

AC:

4421

AN:

19236

East Asian (EAS)

AF:

0.123

AC:

4686

AN:

37984

South Asian (SAS)

AF:

0.216

AC:

14333

AN:

66392

European-Finnish (FIN)

AF:

0.141

AC:

6490

AN:

46042

Middle Eastern (MID)

AF:

0.167

AC:

566

AN:

3382

European-Non Finnish (NFE)

AF:

0.133

AC:

117088

AN:

877182

Other (OTH)

AF:

0.150

AC:

7417

AN:

49446

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

6643

13287

19930

26574

33217

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4128

8256

12384

16512

20640

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.137

AC:

20838

AN:

152074

Hom.:

1488

Cov.:

AF XY:

0.136

AC XY:

10131

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.140

AC:

5807

AN:

41478

American (AMR)

AF:

0.106

AC:

1618

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.229

AC:

794

AN:

3468

East Asian (EAS)

AF:

0.123

AC:

637

AN:

5176

South Asian (SAS)

AF:

0.195

AC:

941

AN:

4824

European-Finnish (FIN)

AF:

0.133

AC:

1403

AN:

10572

Middle Eastern (MID)

AF:

0.180

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.135

AC:

9154

AN:

67966

Other (OTH)

AF:

0.129

AC:

272

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

903

1806

2710

3613

4516

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

234

468

702

936

1170

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.131

Hom.:

1880

Bravo

AF:

0.136

Asia WGS

AF:

0.149

AC:

520

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

(source)

DANN

Benign

0.75

PhyloP100

0.65

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over