rs883180

chr16-55578365-G-Achr16-55578365-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017839.5(LPCAT2):c.1315-744G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 151,866 control chromosomes in the GnomAD database, including 22,168 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 0.54 (22168 hom., cov: 32)
• Consequence: LPCAT2 NM_017839.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LPCAT2	NM_017839.5	c.1315-744G>A		intron_variant		ENST00000262134.10
LPCAT2	XM_011523169.4	c.505-744G>A		intron_variant
LPCAT2	XM_047434277.1	c.1147-744G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LPCAT2	ENST00000262134.10	c.1315-744G>A		intron_variant		1	NM_017839.5	P1
LPCAT2	ENST00000566915.5	n.1397-744G>A		intron_variant, non_coding_transcript_variant		1
LPCAT2	ENST00000565056.1	n.189-744G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81447 AN: 151748 Hom.: 22152 Cov.: 32

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.537 AC: 81505 AN: 151866 Hom.: 22168 Cov.: 32 AF XY: 0.540 AC XY: 40054 AN XY: 74194

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.538

Alfa AF: 0.516 Hom.: 9335

Bravo AF: 0.537

Asia WGS AF: 0.733 AC: 2550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.88
Dann	Benign	0.75

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

Publications

LitVar

Other links and lift over

dbSNP: rs883180; hg19: chr16-55612277;