ENST00000335388.5:n.1505+3032A>G

Variant names:

• chr6-160474097-T-C
• rs2457550
• ENST00000335388.5:n.1505+3032A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000335388.5(LPAL2):​n.1505+3032A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 151,750 control chromosomes in the GnomAD database, including 6,414 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 0.27 (6414 hom., cov: 32)
• Consequence: LPAL2 ENST00000335388.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.425
• Publications: 2 publications found

Genes affected

LPAL2 (HGNC:):

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000335388.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPAL2	NR_028092.1		n.1505+3032A>G		intron	N/A
	LPAL2	NR_028093.1		n.1505+3032A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPAL2	ENST00000335388.5	TSL:1	n.1505+3032A>G		intron	N/A
	LPAL2	ENST00000435757.6	TSL:1	n.1504+3033A>G		intron	N/A
	LPAL2	ENST00000454031.6	TSL:6	n.1572+3032A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41523 AN: 151632 Hom.: 6406 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.274 AC: 41555 AN: 151750 Hom.: 6414 Cov.: 32 AF XY: 0.279 AC XY: 20657 AN XY: 74136

African (AFR) AF: 0.142 AC: 5915 AN: 41534

American (AMR) AF: 0.368 AC: 5612 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1127 AN: 3466

East Asian (EAS) AF: 0.528 AC: 2736 AN: 5178

South Asian (SAS) AF: 0.395 AC: 1896 AN: 4800

European-Finnish (FIN) AF: 0.304 AC: 3200 AN: 10536

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.297 AC: 20121 AN: 67672

Other (OTH) AF: 0.309 AC: 652 AN: 2108

Alfa AF: 0.296 Hom.: 3027

Bravo AF: 0.277

Asia WGS AF: 0.427 AC: 1473 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.2
DANN	Benign	0.49
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs2457550; hg19: chr6-160895129;