chr6-160473333-T-C

Variant names:

• chr6-160473333-T-C
• rs2255830
• ENST00000335388.5:n.1505+3796A>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+3796A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,774 control chromosomes in the GnomAD database, including 17,081 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 0.45 (17081 hom., cov: 33)
• Consequence: LPAL2 ENST00000335388.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.86 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+3796A>G		intron	N/A
	LPAL2	NR_028093.1		n.1505+3796A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPAL2	ENST00000335388.5	TSL:1	n.1505+3796A>G		intron	N/A
	LPAL2	ENST00000435757.6	TSL:1	n.1504+3797A>G		intron	N/A
	LPAL2	ENST00000454031.6	TSL:6	n.1572+3796A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67931 AN: 151656 Hom.: 17061 Cov.: 33

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.448 AC: 67976 AN: 151774 Hom.: 17081 Cov.: 33 AF XY: 0.455 AC XY: 33761 AN XY: 74176

African (AFR) AF: 0.228 AC: 9450 AN: 41490

American (AMR) AF: 0.565 AC: 8615 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1756 AN: 3462

East Asian (EAS) AF: 0.882 AC: 4564 AN: 5176

South Asian (SAS) AF: 0.661 AC: 3187 AN: 4824

European-Finnish (FIN) AF: 0.483 AC: 5102 AN: 10562

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33645 AN: 67688

Other (OTH) AF: 0.497 AC: 1048 AN: 2108

Alfa AF: 0.472 Hom.: 2214

Bravo AF: 0.447

Asia WGS AF: 0.754 AC: 2609 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.7
DANN	Benign	0.88
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs2255830; hg19: chr6-160894365;