6-160458599-T-C

Position:

• chr6-160458599-T-C

Variant summary

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

The ENST00000454031.6(LPAL2):​n.2222+457A>G 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 0.258 in 152,140 control chromosomes in the GnomAD database, including 5,438 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 0.26 (5438 hom., cov: 32)
• Consequence: LPAL2 ENST00000454031.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 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.2222+457A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39265 AN: 152022 Hom.: 5439 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.258 AC: 39276 AN: 152140 Hom.: 5438 Cov.: 32 AF XY: 0.262 AC XY: 19474 AN XY: 74386

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.297

Alfa AF: 0.271 Hom.: 702

Bravo AF: 0.249

Asia WGS AF: 0.390 AC: 1354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1567438; hg19: chr6-160879631;