rs8054459

Variant names:

• chr16-55510637-G-A
• rs8054459
• NM_017839.5:c.171+1285G>A

Variant summary

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

The NM_017839.5(LPCAT2):​c.171+1285G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 151,896 control chromosomes in the GnomAD database, including 18,073 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 0.48 (18073 hom., cov: 31)
• Consequence: LPCAT2 NM_017839.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 9 publications found

Genes affected

LPCAT2 (HGNC:26032): (lysophosphatidylcholine acyltransferase 2) This gene encodes a member of the lysophospholipid acyltransferase family. The encoded enzyme may function in two ways: to catalyze the biosynthesis of platelet-activating factor (1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine) from 1-O-alkyl-sn-glycero-3-phosphocholine, and to catalyze the synthesis of glycerophospholipid precursors from arachidonyl-CoA and lysophosphatidylcholine. The encoded protein may function in membrane biogenesis and production of platelet-activating factor in inflammatory cells. The enzyme may localize to the endoplasmic reticulum and the Golgi. [provided by RefSeq, Feb 2009]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017839.5. 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
	LPCAT2	NM_017839.5	MANE Select	c.171+1285G>A		intron	N/A	NP_060309.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPCAT2	ENST00000262134.10	TSL:1 MANE Select	c.171+1285G>A		intron	N/A	ENSP00000262134.5	Q7L5N7-1
	LPCAT2	ENST00000947554.1		c.171+1285G>A		intron	N/A	ENSP00000617613.1
	LPCAT2	ENST00000929287.1		c.171+1285G>A		intron	N/A	ENSP00000599346.1

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72621 AN: 151778 Hom.: 18053 Cov.: 31

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.478 AC: 72680 AN: 151896 Hom.: 18073 Cov.: 31 AF XY: 0.474 AC XY: 35208 AN XY: 74210

African (AFR) AF: 0.348 AC: 14412 AN: 41366

American (AMR) AF: 0.534 AC: 8148 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2104 AN: 3466

East Asian (EAS) AF: 0.325 AC: 1678 AN: 5170

South Asian (SAS) AF: 0.415 AC: 1995 AN: 4812

European-Finnish (FIN) AF: 0.481 AC: 5079 AN: 10550

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37393 AN: 67950

Other (OTH) AF: 0.519 AC: 1093 AN: 2106

Alfa AF: 0.531 Hom.: 11038

Bravo AF: 0.479

Asia WGS AF: 0.375 AC: 1304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.7
DANN	Benign	0.70
PhyloP100		0.091
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs8054459; hg19: chr16-55544549;