Variant 6-160490876-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000335388.5(LPAL2):n.508+1905G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 151,940 control chromosomes in the GnomAD database, including 16,758 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 ( 16758 hom., cov: 32)

Consequence

LPAL2
ENST00000335388.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.661

Variant links:

Genes affected

LPAL2 (HGNC:):

LPAL2 links:

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]

LPAL2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LPAL2	NR_028092.1 link	n.508+1905G>A		intron_variant
LPAL2	NR_028093.1 link	n.508+1905G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
LPAL2	ENST00000335388.5 link	n.508+1905G>A	intron_variant	1
LPAL2	ENST00000435757.6 link	n.508+1905G>A	intron_variant	1
LPAL2	ENST00000454031.6 link	n.549+487G>A	intron_variant	6

Frequencies

GnomAD3 genomes

AF:

0.442

AC:

67141

AN:

151822

Hom.:

16737

Cov.:

show subpopulations

Gnomad AFR

AF:

0.221

Gnomad AMI

AF:

0.490

Gnomad AMR

AF:

0.558

Gnomad ASJ

AF:

0.502

Gnomad EAS

AF:

0.880

Gnomad SAS

AF:

0.661

Gnomad FIN

AF:

0.482

Gnomad MID

AF:

0.522

Gnomad NFE

AF:

0.491

Gnomad OTH

AF:

0.489

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

GnomAD4 genome

AF:

0.442

AC:

67189

AN:

151940

Hom.:

16758

Cov.:

AF XY:

0.450

AC XY:

33391

AN XY:

74216

show subpopulations

Gnomad4 AFR

AF:

0.221

Gnomad4 AMR

AF:

0.559

Gnomad4 ASJ

AF:

0.502

Gnomad4 EAS

AF:

0.880

Gnomad4 SAS

AF:

0.661

Gnomad4 FIN

AF:

0.482

Gnomad4 NFE

AF:

0.491

Gnomad4 OTH

AF:

0.493

Alfa

AF:

0.485

Hom.:

4091

Bravo

AF:

0.440

Asia WGS

AF:

0.753

AC:

2617

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.47

DANN

Benign

0.75

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over