6-160497382-A-T

Position:

• chr6-160497382-A-T

Variant summary

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

The NR_028093.1(LPAL2):​n.326+3399T>A 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 0.242 in 152,136 control chromosomes in the GnomAD database, including 4,663 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 0.24 (4663 hom., cov: 33)
• Consequence: LPAL2 NR_028093.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.695

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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LPAL2	NR_028093.1	n.326+3399T>A		intron_variant, non_coding_transcript_variant
LPAL2	NR_028092.1	n.326+3399T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LPAL2	ENST00000435757.6	n.326+3399T>A		intron_variant, non_coding_transcript_variant		1
LPAL2	ENST00000454031.6	n.209+3399T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36762 AN: 152018 Hom.: 4654 Cov.: 33

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.242 AC: 36795 AN: 152136 Hom.: 4663 Cov.: 33 AF XY: 0.241 AC XY: 17946 AN XY: 74388

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.249

Alfa AF: 0.109 Hom.: 177

Bravo AF: 0.245

Asia WGS AF: 0.353 AC: 1229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7754188; hg19: chr6-160918414;