ENST00000335388.5:n.1505+3796A>G

Variant names:

• chr6-160473333-T-C
• rs2255830
• ENST00000335388.5:n.1505+3796A>G

Variant summary

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

The ENST00000335388.5(LPAL2):​n.1505+3796A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,774 control chromosomes in the GnomAD database, including 17,081 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 0.45 (17081 hom., cov: 33)
• Consequence: LPAL2 ENST00000335388.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358

Genes affected

LPAL2 (HGNC:):

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LPAL2	NR_028092.1	n.1505+3796A>G		intron_variant	Intron 9 of 9
LPAL2	NR_028093.1	n.1505+3796A>G		intron_variant	Intron 9 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LPAL2	ENST00000335388.5	n.1505+3796A>G		intron_variant	Intron 9 of 9	1
LPAL2	ENST00000435757.6	n.1504+3797A>G		intron_variant	Intron 9 of 9	1
LPAL2	ENST00000454031.6	n.1572+3796A>G		intron_variant	Intron 10 of 16	6
LPAL2	ENST00000606083.1	n.67+3796A>G		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67931 AN: 151656 Hom.: 17061 Cov.: 33

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.448 AC: 67976 AN: 151774 Hom.: 17081 Cov.: 33 AF XY: 0.455 AC XY: 33761 AN XY: 74176

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.565

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.882

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.497

Alfa AF: 0.472 Hom.: 2214

Bravo AF: 0.447

Asia WGS AF: 0.754 AC: 2609 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.7
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2255830; hg19: chr6-160894365;