rs2063347

chr6-160460997-G-Achr6-160460997-G-C

Variant summary

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

The ENST00000454031.6(LPAL2):n.2115+258C>T 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 0.291 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

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=-0.92).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LPAL2	ENST00000454031.6	n.2115+258C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0871

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.294

Alfa AF: 0.351 Hom.: 10785

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2063347; hg19: chr6-160882029;