rs3127599

Variant names:

• chr6-160486102-C-A
• rs3127599
• ENST00000335388.5:n.691-128G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-160486102-C-A
• chr6-160486102-C-G
• chr6-160486102-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000335388.5(LPAL2):​n.691-128G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LPAL2 ENST00000335388.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPAL2	NR_028092.1		n.691-128G>T		intron	N/A
	LPAL2	NR_028093.1		n.691-128G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPAL2	ENST00000335388.5	TSL:1	n.691-128G>T		intron	N/A
	LPAL2	ENST00000435757.6	TSL:1	n.691-128G>T		intron	N/A
	LPAL2	ENST00000454031.6	TSL:6	n.732-128G>T		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 152588 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 84548

African (AFR) AF: 0.00 AC: 0 AN: 4892

American (AMR) AF: 0.00 AC: 0 AN: 11008

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3102

East Asian (EAS) AF: 0.00 AC: 0 AN: 8794

South Asian (SAS) AF: 0.00 AC: 0 AN: 24424

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7422

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 464

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 84944

Other (OTH) AF: 0.00 AC: 0 AN: 7538

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.090
PhyloP100		-0.064

Splicing

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

Other links and lift over

dbSNP: rs3127599; hg19: chr6-160907134;