16-55545524-A-C

Position:

• chr16-55545524-A-C

Variant summary

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

The NM_017839.5(LPCAT2):​c.853-211A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0724 in 398,670 control chromosomes in the GnomAD database, including 1,575 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 0.089 (874 hom., cov: 32)
  • Exomes 𝑓: 0.062 (701 hom.)
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LPCAT2	NM_017839.5	c.853-211A>C		intron_variant		ENST00000262134.10
LPCAT2	XM_011523169.4	c.43-211A>C		intron_variant
LPCAT2	XM_047434277.1	c.685-211A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LPCAT2	ENST00000262134.10	c.853-211A>C		intron_variant		1	NM_017839.5	P1
LPCAT2	ENST00000566915.5	n.935-211A>C		intron_variant, non_coding_transcript_variant		1
LPCAT2	ENST00000563095.5	n.40A>C		non_coding_transcript_exon_variant	1/4	3

Frequencies

GnomAD3 genomes AF: 0.0888 AC: 13493 AN: 152012 Hom.: 862 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0587

Gnomad ASJ AF: 0.0694

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0196

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0500

Gnomad OTH AF: 0.0947

GnomAD4 exome AF: 0.0622 AC: 15341 AN: 246540 Hom.: 701 Cov.: 2 AF XY: 0.0622 AC XY: 7884 AN XY: 126672

Gnomad4 AFR exome AF: 0.173

Gnomad4 AMR exome AF: 0.0631

Gnomad4 ASJ exome AF: 0.0619

Gnomad4 EAS exome AF: 0.137

Gnomad4 SAS exome AF: 0.115

Gnomad4 FIN exome AF: 0.0214

Gnomad4 NFE exome AF: 0.0496

Gnomad4 OTH exome AF: 0.0762

GnomAD4 genome AF: 0.0890 AC: 13540 AN: 152130 Hom.: 874 Cov.: 32 AF XY: 0.0882 AC XY: 6559 AN XY: 74376

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.0586

Gnomad4 ASJ AF: 0.0694

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.0196

Gnomad4 NFE AF: 0.0500

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0657 Hom.: 235

Bravo AF: 0.0980

Asia WGS AF: 0.184 AC: 638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.3
DANN	Benign	0.77

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: rs10521319; hg19: chr16-55579436;