rs8182127

Positions:

• chr16-55535685-A-G

Variant summary

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

The NM_017839.5(LPCAT2):​c.797+1208A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0871 in 152,236 control chromosomes in the GnomAD database, including 736 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 0.087 (736 hom., cov: 32)
• Consequence: LPCAT2 NM_017839.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

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 (AFR) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LPCAT2	NM_017839.5	c.797+1208A>G		intron_variant		ENST00000262134.10	NP_060309.2
LPCAT2	XM_005256006.4	c.797+1208A>G		intron_variant			XP_005256063.1
LPCAT2	XM_011523169.4	c.-14+1208A>G		intron_variant			XP_011521471.1
LPCAT2	XM_047434277.1	c.629+1208A>G		intron_variant			XP_047290233.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LPCAT2	ENST00000262134.10	c.797+1208A>G		intron_variant		1	NM_017839.5	ENSP00000262134	P1
LPCAT2	ENST00000566915.5	n.879+1208A>G		intron_variant, non_coding_transcript_variant		1
LPCAT2	ENST00000564084.1	c.370+1208A>G		intron_variant		3		ENSP00000457496

Frequencies

GnomAD3 genomes AF: 0.0870 AC: 13240 AN: 152116 Hom.: 729 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0818

Gnomad ASJ AF: 0.0974

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0199

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0539

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.0871 AC: 13262 AN: 152236 Hom.: 736 Cov.: 32 AF XY: 0.0871 AC XY: 6481 AN XY: 74414

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.0816

Gnomad4 ASJ AF: 0.0974

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0199

Gnomad4 NFE AF: 0.0539

Gnomad4 OTH AF: 0.111

Alfa AF: 0.0666 Hom.: 353

Bravo AF: 0.0965

Asia WGS AF: 0.162 AC: 563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.67

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: rs8182127; hg19: chr16-55569597;