rs11541237

chr10-73771204-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_198597.3(SEC24C):c.*109C>T variant causes a 3 prime UTR 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 NM_198597.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.651

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SEC24C	NM_198597.3	c.*109C>T		3_prime_UTR_variant	23/23	ENST00000345254.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SEC24C	ENST00000345254.9	c.*109C>T		3_prime_UTR_variant	23/23	1	NM_198597.3	P1
	ENST00000623453.1	n.1659G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20784 AN: 151956 Hom.: 1470 Cov.: 32

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.: 15 AF XY: 0.142 AC XY: 82207 AN XY: 577752

Gnomad4 AFR exome AF: 0.140

Gnomad4 AMR exome AF: 0.0918

Gnomad4 ASJ exome AF: 0.230

Gnomad4 EAS exome AF: 0.123

Gnomad4 SAS exome AF: 0.216

Gnomad4 FIN exome AF: 0.141

Gnomad4 NFE exome AF: 0.133

Gnomad4 OTH exome AF: 0.150

GnomAD4 genome AF: 0.137 AC: 20838 AN: 152074 Hom.: 1488 Cov.: 32 AF XY: 0.136 AC XY: 10131 AN XY: 74338

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.129

Alfa AF: 0.130 Hom.: 1452

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	13
Dann	Benign	0.75

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

Other links and lift over

dbSNP: rs11541237; hg19: chr10-75530962;