16-5011947-T-C

Variant names:

• chr16-5011947-T-C
• rs1558561
• NM_014692.2:c.1979+674T>C

Variant summary

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

The NM_014692.2(SEC14L5):​c.1979+674T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 152,054 control chromosomes in the GnomAD database, including 16,404 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 0.46 (16404 hom., cov: 32)
• Consequence: SEC14L5 NM_014692.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124
• Publications: 4 publications found

Genes affected

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

ENSG00000267072 (HGNC:):

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 = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEC14L5	NM_014692.2	c.1979+674T>C		intron_variant	Intron 15 of 15	ENST00000251170.12	NP_055507.1
SEC14L5	XM_024450497.2	c.1979+674T>C		intron_variant	Intron 15 of 15		XP_024306265.1
SEC14L5	XM_024450498.2	c.1979+674T>C		intron_variant	Intron 15 of 15		XP_024306266.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEC14L5	ENST00000251170.12	c.1979+674T>C		intron_variant	Intron 15 of 15	1	NM_014692.2	ENSP00000251170.6
ENSG00000267072	ENST00000588778.1	n.365+674T>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69556 AN: 151936 Hom.: 16377 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.458 AC: 69620 AN: 152054 Hom.: 16404 Cov.: 32 AF XY: 0.451 AC XY: 33509 AN XY: 74322

African (AFR) AF: 0.572 AC: 23701 AN: 41464

American (AMR) AF: 0.352 AC: 5366 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1633 AN: 3468

East Asian (EAS) AF: 0.432 AC: 2227 AN: 5152

South Asian (SAS) AF: 0.385 AC: 1857 AN: 4822

European-Finnish (FIN) AF: 0.355 AC: 3758 AN: 10582

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29502 AN: 67986

Other (OTH) AF: 0.455 AC: 961 AN: 2110

Alfa AF: 0.441 Hom.: 43710

Bravo AF: 0.467

Asia WGS AF: 0.392 AC: 1365 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	5.1
DANN	Benign	0.67
PhyloP100		-0.12
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: rs1558561; hg19: chr16-5061948;