chr6-160486102-C-T

Variant names:

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

Variant summary

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

The ENST00000335388.5(LPAL2):​n.691-128G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 303,828 control chromosomes in the GnomAD database, including 12,204 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 (6382 hom., cov: 33)
  • Exomes 𝑓: 0.27 (5822 hom.)
• Consequence: LPAL2 ENST00000335388.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640
• Publications: 46 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.296 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.691-128G>A		intron	N/A
	LPAL2	NR_028093.1		n.691-128G>A		intron	N/A

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42557 AN: 151608 Hom.: 6376 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.266

GnomAD4 exome AF: 0.269 AC: 40885 AN: 152100 Hom.: 5822 AF XY: 0.266 AC XY: 22401 AN XY: 84294

African (AFR) AF: 0.278 AC: 1350 AN: 4862

American (AMR) AF: 0.150 AC: 1644 AN: 10980

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 919 AN: 3090

East Asian (EAS) AF: 0.116 AC: 1017 AN: 8778

South Asian (SAS) AF: 0.230 AC: 5603 AN: 24354

European-Finnish (FIN) AF: 0.340 AC: 2518 AN: 7402

Middle Eastern (MID) AF: 0.250 AC: 116 AN: 464

European-Non Finnish (NFE) AF: 0.302 AC: 25572 AN: 84646

Other (OTH) AF: 0.285 AC: 2146 AN: 7524

GnomAD4 genome AF: 0.281 AC: 42575 AN: 151728 Hom.: 6382 Cov.: 33 AF XY: 0.279 AC XY: 20675 AN XY: 74134

African (AFR) AF: 0.291 AC: 11975 AN: 41190

American (AMR) AF: 0.195 AC: 2979 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1005 AN: 3462

East Asian (EAS) AF: 0.114 AC: 590 AN: 5170

South Asian (SAS) AF: 0.231 AC: 1113 AN: 4816

European-Finnish (FIN) AF: 0.345 AC: 3636 AN: 10546

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20357 AN: 67960

Other (OTH) AF: 0.264 AC: 558 AN: 2110

Alfa AF: 0.286 Hom.: 11554

Bravo AF: 0.267

Asia WGS AF: 0.158 AC: 551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.12
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;