6-160497263-A-T

Variant names:

• chr6-160497263-A-T
• rs7754014
• ENST00000335388.5:n.326+3518T>A

Variant summary

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

The ENST00000335388.5(LPAL2):​n.326+3518T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 151,968 control chromosomes in the GnomAD database, including 6,846 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 0.28 (6846 hom., cov: 32)
• Consequence: LPAL2 ENST00000335388.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09
• Publications: 7 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.426 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPAL2	NR_028092.1		n.326+3518T>A		intron	N/A
	LPAL2	NR_028093.1		n.326+3518T>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPAL2	ENST00000335388.5	TSL:1	n.326+3518T>A		intron	N/A
	LPAL2	ENST00000435757.6	TSL:1	n.326+3518T>A		intron	N/A
	LPAL2	ENST00000454031.6	TSL:6	n.209+3518T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42898 AN: 151852 Hom.: 6817 Cov.: 32

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.283 AC: 42971 AN: 151968 Hom.: 6846 Cov.: 32 AF XY: 0.280 AC XY: 20815 AN XY: 74282

African (AFR) AF: 0.431 AC: 17843 AN: 41394

American (AMR) AF: 0.242 AC: 3694 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 741 AN: 3472

East Asian (EAS) AF: 0.342 AC: 1766 AN: 5158

South Asian (SAS) AF: 0.268 AC: 1288 AN: 4810

European-Finnish (FIN) AF: 0.178 AC: 1881 AN: 10580

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.217 AC: 14755 AN: 67980

Other (OTH) AF: 0.280 AC: 590 AN: 2106

Alfa AF: 0.116 Hom.: 186

Bravo AF: 0.292

Asia WGS AF: 0.352 AC: 1226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.16
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs7754014; hg19: chr6-160918295;