ENST00000335388.5:n.326+247A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000335388.5(LPAL2):​n.326+247A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 152,018 control chromosomes in the GnomAD database, including 16,717 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 0.44 ( 16717 hom., cov: 32)

Consequence

LPAL2
ENST00000335388.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0560
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 = 0.86 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LPAL2NR_028092.1 linkn.326+247A>C intron_variant Intron 2 of 9
LPAL2NR_028093.1 linkn.326+247A>C intron_variant Intron 2 of 9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LPAL2ENST00000335388.5 linkn.326+247A>C intron_variant Intron 2 of 9 1
LPAL2ENST00000435757.6 linkn.326+247A>C intron_variant Intron 2 of 9 1
LPAL2ENST00000454031.6 linkn.209+247A>C intron_variant Intron 2 of 16 6

Frequencies

GnomAD3 genomes
AF:
0.440
AC:
66856
AN:
151900
Hom.:
16696
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.213
Gnomad AMI
AF:
0.490
Gnomad AMR
AF:
0.557
Gnomad ASJ
AF:
0.503
Gnomad EAS
AF:
0.881
Gnomad SAS
AF:
0.662
Gnomad FIN
AF:
0.481
Gnomad MID
AF:
0.522
Gnomad NFE
AF:
0.491
Gnomad OTH
AF:
0.485
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.440
AC:
66904
AN:
152018
Hom.:
16717
Cov.:
32
AF XY:
0.448
AC XY:
33279
AN XY:
74304
show subpopulations
Gnomad4 AFR
AF:
0.213
Gnomad4 AMR
AF:
0.558
Gnomad4 ASJ
AF:
0.503
Gnomad4 EAS
AF:
0.882
Gnomad4 SAS
AF:
0.662
Gnomad4 FIN
AF:
0.481
Gnomad4 NFE
AF:
0.491
Gnomad4 OTH
AF:
0.490
Alfa
AF:
0.478
Hom.:
17183
Bravo
AF:
0.438
Asia WGS
AF:
0.755
AC:
2624
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
1.6
DANN
Benign
0.26

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9457930; hg19: chr6-160921566; API