rs2302553

Variant names:

• chr16-5006294-A-C
• rs2302553
• NM_014692.2:c.1437+246A>C

Your query was ambiguous. Multiple possible variants found:

• chr16-5006294-A-C
• chr16-5006294-A-G
• chr16-5006294-A-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.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
• Publications: 4 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=-0.82).
• 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 rank	MANE	Protein	UniProt
SEC14L5	NM_014692.2	c.1437+246A>C		intron_variant	Intron 12 of 15	ENST00000251170.12	NP_055507.1
SEC14L5	XM_024450497.2	c.1437+246A>C		intron_variant	Intron 12 of 15		XP_024306265.1
SEC14L5	XM_024450498.2	c.1437+246A>C		intron_variant	Intron 12 of 15		XP_024306266.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEC14L5	ENST00000251170.12	c.1437+246A>C		intron_variant	Intron 12 of 15	1	NM_014692.2	ENSP00000251170.6

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

African (AFR) AF: 0.542 AC: 22487 AN: 41502

American (AMR) AF: 0.422 AC: 6456 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1268 AN: 3466

East Asian (EAS) AF: 0.188 AC: 975 AN: 5180

South Asian (SAS) AF: 0.211 AC: 1018 AN: 4828

European-Finnish (FIN) AF: 0.421 AC: 4457 AN: 10584

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21102 AN: 67996

Other (OTH) AF: 0.369 AC: 780 AN: 2112

Alfa AF: 0.326 Hom.: 7510

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
PhyloP100		-0.75
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: rs2302553; hg19: chr16-5056295;