rs3127599

Positions:

• chr6-160486102-C-T

Variant summary

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

The NR_028093.1(LPAL2):​n.691-128G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 303,828 control chromosomes in the GnomAD database, including 12,204 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 0.28 (6382 hom., cov: 33)
  • Exomes 𝑓: 0.27 (5822 hom.)
• Consequence: LPAL2 NR_028093.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LPAL2	NR_028093.1	n.691-128G>A		intron_variant, non_coding_transcript_variant
LPAL2	NR_028092.1	n.691-128G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LPAL2	ENST00000335388.5	n.691-128G>A		intron_variant, non_coding_transcript_variant		1
LPAL2	ENST00000435757.6	n.691-128G>A		intron_variant, non_coding_transcript_variant		1
LPAL2	ENST00000454031.6	n.732-128G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42557 AN: 151608 Hom.: 6376 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.266

GnomAD4 exome AF: 0.269 AC: 40885 AN: 152100 Hom.: 5822 AF XY: 0.266 AC XY: 22401 AN XY: 84294

Gnomad4 AFR exome AF: 0.278

Gnomad4 AMR exome AF: 0.150

Gnomad4 ASJ exome AF: 0.297

Gnomad4 EAS exome AF: 0.116

Gnomad4 SAS exome AF: 0.230

Gnomad4 FIN exome AF: 0.340

Gnomad4 NFE exome AF: 0.302

Gnomad4 OTH exome AF: 0.285

GnomAD4 genome AF: 0.281 AC: 42575 AN: 151728 Hom.: 6382 Cov.: 33 AF XY: 0.279 AC XY: 20675 AN XY: 74134

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.264

Alfa AF: 0.278 Hom.: 1181

Bravo AF: 0.267

Asia WGS AF: 0.158 AC: 551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3127599; hg19: chr6-160907134;