rs3815490

Variant names:

• chr16-5010567-C-T
• rs3815490
• NM_014692.2:c.1801-528C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014692.2(SEC14L5):​c.1801-528C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,060 control chromosomes in the GnomAD database, including 4,945 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 0.23 (4945 hom., cov: 31)
• Consequence: SEC14L5 NM_014692.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEC14L5	NM_014692.2	c.1801-528C>T		intron_variant	Intron 14 of 15	ENST00000251170.12	NP_055507.1
SEC14L5	XM_024450497.2	c.1801-528C>T		intron_variant	Intron 14 of 15		XP_024306265.1
SEC14L5	XM_024450498.2	c.1801-528C>T		intron_variant	Intron 14 of 15		XP_024306266.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEC14L5	ENST00000251170.12	c.1801-528C>T		intron_variant	Intron 14 of 15	1	NM_014692.2	ENSP00000251170.6

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35524 AN: 151942 Hom.: 4945 Cov.: 31

Gnomad AFR AF: 0.0927

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.234 AC: 35529 AN: 152060 Hom.: 4945 Cov.: 31 AF XY: 0.241 AC XY: 17893 AN XY: 74322

African (AFR) AF: 0.0925 AC: 3838 AN: 41490

American (AMR) AF: 0.342 AC: 5226 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1174 AN: 3472

East Asian (EAS) AF: 0.144 AC: 747 AN: 5170

South Asian (SAS) AF: 0.165 AC: 794 AN: 4808

European-Finnish (FIN) AF: 0.411 AC: 4341 AN: 10560

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18574 AN: 67980

Other (OTH) AF: 0.248 AC: 523 AN: 2112

Alfa AF: 0.256 Hom.: 4061

Bravo AF: 0.223

Asia WGS AF: 0.158 AC: 550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.53
PhyloP100		0.072
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3815490; hg19: chr16-5060568;