rs2972284

Variant names:

• chr16-5018151-C-T
• rs2972284
• NM_014692.2:c.*3181C>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.*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
• Publications: 11 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=-0.92).
• 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 rank	MANE	Protein	UniProt
SEC14L5	NM_014692.2	c.*3181C>T		3_prime_UTR_variant	Exon 16 of 16	ENST00000251170.12	NP_055507.1
SEC14L5	XM_024450497.2	c.*3181C>T		3_prime_UTR_variant	Exon 16 of 16		XP_024306265.1
SEC14L5	XM_024450498.2	c.*3181C>T		3_prime_UTR_variant	Exon 16 of 16		XP_024306266.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEC14L5	ENST00000251170.12	c.*3181C>T		3_prime_UTR_variant	Exon 16 of 16	1	NM_014692.2	ENSP00000251170.6
ENSG00000267072	ENST00000588778.1	n.365+6878C>T		intron_variant	Intron 1 of 1	3

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

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.147 AC: 5 AN: 34

Other (OTH) AF: 0.250 AC: 1 AN: 4

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

African (AFR) AF: 0.448 AC: 18591 AN: 41480

American (AMR) AF: 0.191 AC: 2922 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 581 AN: 3466

East Asian (EAS) AF: 0.299 AC: 1546 AN: 5166

South Asian (SAS) AF: 0.246 AC: 1186 AN: 4814

European-Finnish (FIN) AF: 0.144 AC: 1518 AN: 10568

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12013 AN: 68000

Other (OTH) AF: 0.243 AC: 512 AN: 2106

Alfa AF: 0.202 Hom.: 6779

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
PhyloP100		-1.2
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: rs2972284; hg19: chr16-5068152;