rs183154

chr16-55575346-G-Achr16-55575346-G-Cchr16-55575346-G-T

Variant summary

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

The NM_017839.5(LPCAT2):c.1314+617G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.951 in 152,224 control chromosomes in the GnomAD database, including 69,037 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 0.95 (69037 hom., cov: 32)
• Consequence: LPCAT2 NM_017839.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.984 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LPCAT2	NM_017839.5	c.1314+617G>A		intron_variant		ENST00000262134.10
LPCAT2	XM_011523169.4	c.504+617G>A		intron_variant
LPCAT2	XM_047434277.1	c.1146+617G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LPCAT2	ENST00000262134.10	c.1314+617G>A		intron_variant		1	NM_017839.5	P1
LPCAT2	ENST00000566915.5	n.1396+617G>A		intron_variant, non_coding_transcript_variant		1
LPCAT2	ENST00000565056.1	n.188+617G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.951 AC: 144629 AN: 152106 Hom.: 68989 Cov.: 32

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.959

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.940

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.958

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

GnomAD4 genome AF: 0.951 AC: 144735 AN: 152224 Hom.: 69037 Cov.: 32 AF XY: 0.950 AC XY: 70732 AN XY: 74438

Gnomad4 AFR AF: 0.866

Gnomad4 AMR AF: 0.959

Gnomad4 ASJ AF: 0.948

Gnomad4 EAS AF: 0.992

Gnomad4 SAS AF: 0.940

Gnomad4 FIN AF: 0.999

Gnomad4 NFE AF: 0.990

Gnomad4 OTH AF: 0.958

Alfa AF: 0.976 Hom.: 29041

Bravo AF: 0.946

Asia WGS AF: 0.962 AC: 3345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.073
Dann	Benign	0.18

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: rs183154; hg19: chr16-55609258;