ENST00000454031.6:n.2115+258C>T

Variant names:

• chr6-160460997-G-A
• rs2063347
• ENST00000454031.6:n.2115+258C>T

Variant summary

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

The ENST00000454031.6(LPAL2):​n.2115+258C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,080 control chromosomes in the GnomAD database, including 7,899 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 0.29 (7899 hom., cov: 33)
• Consequence: LPAL2 ENST00000454031.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990
• Publications: 19 publications found

Genes affected

LPAL2 (HGNC:21210): (lipoprotein(a) like 2 (pseudogene)) Apolipoprotein(a) is the distinguishing protein moiety of lipoprotein(a), of which elevated plasma levels are correlated with an increased risk of atherosclerosis. This gene is similar to the lipoprotein, Lp(a) gene, but all transcripts produced by this gene contain a truncated open reading frame and are candidates for nonsense-mediated decay. Consequently, this gene is considered to be a pseudogene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2009]

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 (EAS) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LPAL2	ENST00000454031.6	n.2115+258C>T		intron_variant	Intron 14 of 16	6

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44164 AN: 151962 Hom.: 7885 Cov.: 33

Gnomad AFR AF: 0.0872

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.291 AC: 44191 AN: 152080 Hom.: 7899 Cov.: 33 AF XY: 0.289 AC XY: 21456 AN XY: 74338

African (AFR) AF: 0.0871 AC: 3616 AN: 41510

American (AMR) AF: 0.435 AC: 6642 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 784 AN: 3472

East Asian (EAS) AF: 0.465 AC: 2407 AN: 5178

South Asian (SAS) AF: 0.276 AC: 1328 AN: 4816

European-Finnish (FIN) AF: 0.298 AC: 3150 AN: 10556

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25209 AN: 67974

Other (OTH) AF: 0.294 AC: 623 AN: 2116

Alfa AF: 0.346 Hom.: 15424

Bravo AF: 0.293

Asia WGS AF: 0.379 AC: 1316 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	0.77
DANN	Benign	0.52
PhyloP100		-0.099

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2063347; hg19: chr6-160882029;