3-10295169-C-T

Variant names:

• chr3-10295169-C-T
• rs1617161
• ENST00000492602.5:n.188-1833G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000492602.5(SEC13):​n.188-1833G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,210 control chromosomes in the GnomAD database, including 1,726 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 (1726 hom., cov: 32)
• Consequence: SEC13 ENST00000492602.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEC13	ENST00000492602.5	n.188-1833G>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20979 AN: 152092 Hom.: 1723 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.130

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.138 AC: 20990 AN: 152210 Hom.: 1726 Cov.: 32 AF XY: 0.140 AC XY: 10397 AN XY: 74414

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.131

Alfa AF: 0.121 Hom.: 306

Bravo AF: 0.135

Asia WGS AF: 0.230 AC: 801 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.0
DANN	Benign	0.72

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1617161; hg19: chr3-10336853;