16-55578365-G-A

Variant names:

• chr16-55578365-G-A
• rs883180
• NM_017839.5:c.1315-744G>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.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
• Publications: 16 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=-0.94).
• 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 rank	MANE	Protein	UniProt
LPCAT2	NM_017839.5	c.1315-744G>A		intron_variant	Intron 12 of 13	ENST00000262134.10	NP_060309.2
LPCAT2	XM_047434277.1	c.1147-744G>A		intron_variant	Intron 12 of 13		XP_047290233.1
LPCAT2	XM_011523169.4	c.505-744G>A		intron_variant	Intron 9 of 10		XP_011521471.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LPCAT2	ENST00000262134.10	c.1315-744G>A		intron_variant	Intron 12 of 13	1	NM_017839.5	ENSP00000262134.5
LPCAT2	ENST00000566915.5	n.1397-744G>A		intron_variant	Intron 7 of 8	1
LPCAT2	ENST00000565056.1	n.189-744G>A		intron_variant	Intron 2 of 3	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

African (AFR) AF: 0.589 AC: 24395 AN: 41392

American (AMR) AF: 0.495 AC: 7543 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1495 AN: 3470

East Asian (EAS) AF: 0.729 AC: 3762 AN: 5164

South Asian (SAS) AF: 0.649 AC: 3116 AN: 4802

European-Finnish (FIN) AF: 0.519 AC: 5471 AN: 10542

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.503 AC: 34175 AN: 67936

Other (OTH) AF: 0.538 AC: 1131 AN: 2104

Alfa AF: 0.515 Hom.: 10328

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
PhyloP100		-0.29
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: rs883180; hg19: chr16-55612277;