rs2192853

chr16-55511434-A-Gchr16-55511434-A-T

Variant summary

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

The NM_017839.5(LPCAT2):c.171+2082A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 152,014 control chromosomes in the GnomAD database, including 20,426 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 0.52 (20426 hom., cov: 32)
• Consequence: LPCAT2 NM_017839.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LPCAT2	NM_017839.5	c.171+2082A>G		intron_variant		ENST00000262134.10
LPCAT2	XM_005256006.4	c.171+2082A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LPCAT2	ENST00000262134.10	c.171+2082A>G		intron_variant		1	NM_017839.5	P1
LPCAT2	ENST00000566911.1	n.281+2082A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78254 AN: 151896 Hom.: 20398 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.515 AC: 78328 AN: 152014 Hom.: 20426 Cov.: 32 AF XY: 0.511 AC XY: 38002 AN XY: 74306

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.545

Alfa AF: 0.415 Hom.: 1113

Bravo AF: 0.519

Asia WGS AF: 0.427 AC: 1478 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.6
Dann	Benign	0.68

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: rs2192853; hg19: chr16-55545346;