rs5753152

Positions:

• chr22-30450636-A-G
• chr22-30450636-A-T

Variant summary

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

The NM_001376914.1(SEC14L3):​c.905-1392T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 152,056 control chromosomes in the GnomAD database, including 38,136 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 0.70 (38136 hom., cov: 31)
• Consequence: SEC14L3 NM_001376914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

Genes affected

SEC14L3 (HGNC:18655): (SEC14 like lipid binding 3) The protein encoded by this gene is highly similar to the protein encoded by the Saccharomyces cerevisiae SEC14 gene. The SEC14 protein is a phophatidylinositol transfer protein that is essential for biogenesis of Golgi-derived transport vesicles, and thus is required for the export of yeast secretory proteins from the Golgi complex. The specific function of this protein has not yet been determined. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]

LOC105372991 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SEC14L3	NM_001376914.1	c.905-1392T>C		intron_variant			NP_001363843.1
SEC14L3	XM_011530128.3	c.1082-1392T>C		intron_variant			XP_011528430.1
LOC105372991	XR_001755491.2	n.258-725A>G		intron_variant
LOC105372991	XR_007068061.1	n.161-725A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SEC14L3	ENST00000403066.5	c.905-1392T>C		intron_variant		2		ENSP00000385941.1

Frequencies

GnomAD3 genomes AF: 0.698 AC: 106073 AN: 151938 Hom.: 38081 Cov.: 31

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.698 AC: 106188 AN: 152056 Hom.: 38136 Cov.: 31 AF XY: 0.705 AC XY: 52399 AN XY: 74328

Gnomad4 AFR AF: 0.858

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.848

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.665

Alfa AF: 0.646 Hom.: 5243

Bravo AF: 0.694

Asia WGS AF: 0.839 AC: 2918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5753152; hg19: chr22-30846623;