rs2302553

Positions:

• chr16-5006294-A-C

Variant summary

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

The NM_014692.2(SEC14L5):​c.1437+246A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 152,156 control chromosomes in the GnomAD database, including 12,298 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 0.39 (12298 hom., cov: 33)
• Consequence: SEC14L5 NM_014692.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.746

Genes affected

SEC14L5 (HGNC:29032): (SEC14 like lipid binding 5)

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 (AFR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SEC14L5	NM_014692.2	c.1437+246A>C		intron_variant		ENST00000251170.12
SEC14L5	XM_024450497.2	c.1437+246A>C		intron_variant
SEC14L5	XM_024450498.2	c.1437+246A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SEC14L5	ENST00000251170.12	c.1437+246A>C		intron_variant		1	NM_014692.2	P1

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58791 AN: 152038 Hom.: 12285 Cov.: 33

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.387 AC: 58851 AN: 152156 Hom.: 12298 Cov.: 33 AF XY: 0.387 AC XY: 28819 AN XY: 74374

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.369

Alfa AF: 0.332 Hom.: 5567

Bravo AF: 0.395

Asia WGS AF: 0.218 AC: 763 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.8
DANN	Benign	0.84

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: rs2302553; hg19: chr16-5056295;