rs2136675

Variant names:

• chr6-160475399-A-C
• rs2136675
• ENST00000335388.5:n.1505+1730T>G

Your query was ambiguous. Multiple possible variants found:

• chr6-160475399-A-C
• chr6-160475399-A-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+1730T>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 152,000 control chromosomes in the GnomAD database, including 6,433 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 (6433 hom., cov: 32)
• Consequence: LPAL2 ENST00000335388.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LPAL2	NR_028092.1	n.1505+1730T>G		intron_variant	Intron 9 of 9
LPAL2	NR_028093.1	n.1505+1730T>G		intron_variant	Intron 9 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LPAL2	ENST00000335388.5	n.1505+1730T>G		intron_variant	Intron 9 of 9	1
LPAL2	ENST00000435757.6	n.1504+1731T>G		intron_variant	Intron 9 of 9	1
LPAL2	ENST00000454031.6	n.1572+1730T>G		intron_variant	Intron 10 of 16	6
LPAL2	ENST00000606083.1	n.67+1730T>G		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41628 AN: 151882 Hom.: 6425 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.274 AC: 41660 AN: 152000 Hom.: 6433 Cov.: 32 AF XY: 0.279 AC XY: 20713 AN XY: 74288

African (AFR) AF: 0.143 AC: 5931 AN: 41506

American (AMR) AF: 0.368 AC: 5618 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1130 AN: 3462

East Asian (EAS) AF: 0.527 AC: 2711 AN: 5148

South Asian (SAS) AF: 0.396 AC: 1909 AN: 4824

European-Finnish (FIN) AF: 0.305 AC: 3221 AN: 10544

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20189 AN: 67938

Other (OTH) AF: 0.310 AC: 653 AN: 2108

Alfa AF: 0.296 Hom.: 7948

Bravo AF: 0.277

Asia WGS AF: 0.426 AC: 1479 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.55
PhyloP100		-0.026

Splicing

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

Other links and lift over

dbSNP: rs2136675; hg19: chr6-160896431;