rs2972284

chr16-5018151-C-T

Variant summary

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

The NM_014692.2(SEC14L5):c.*3181C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,126 control chromosomes in the GnomAD database, including 6,240 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 0.26 (6239 hom., cov: 33)
  • Exomes 𝑓: 0.16 (1 hom.)
• Consequence: SEC14L5 NM_014692.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SEC14L5	NM_014692.2	c.*3181C>T		3_prime_UTR_variant	16/16	ENST00000251170.12
SEC14L5	XM_024450497.2	c.*3181C>T		3_prime_UTR_variant	16/16
SEC14L5	XM_024450498.2	c.*3181C>T		3_prime_UTR_variant	16/16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SEC14L5	ENST00000251170.12	c.*3181C>T		3_prime_UTR_variant	16/16	1	NM_014692.2	P1

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39021 AN: 151964 Hom.: 6214 Cov.: 33

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.246

GnomAD4 exome AF: 0.159 AC: 7 AN: 44 Hom.: 1 Cov.: 0 AF XY: 0.200 AC XY: 6 AN XY: 30

Gnomad4 AMR exome AF: 0.00

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.147

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.257 AC: 39094 AN: 152082 Hom.: 6239 Cov.: 33 AF XY: 0.256 AC XY: 19001 AN XY: 74346

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.243

Alfa AF: 0.191 Hom.: 4374

Bravo AF: 0.269

Asia WGS AF: 0.227 AC: 793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.2
Dann	Benign	0.54

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: rs2972284; hg19: chr16-5068152;