rs8053806

Positions:

• chr16-55515485-C-A

Variant summary

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

The ENST00000262134.10(LPCAT2):​c.171+6133C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151,790 control chromosomes in the GnomAD database, including 13,022 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 0.40 (13022 hom., cov: 33)
• Consequence: LPCAT2 ENST00000262134.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.379

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LPCAT2	NM_017839.5	c.171+6133C>A		intron_variant		ENST00000262134.10	NP_060309.2
LPCAT2	XM_005256006.4	c.171+6133C>A		intron_variant			XP_005256063.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LPCAT2	ENST00000262134.10	c.171+6133C>A		intron_variant		1	NM_017839.5	ENSP00000262134	P1
LPCAT2	ENST00000566911.1	n.281+6133C>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60497 AN: 151670 Hom.: 13017 Cov.: 33

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.399 AC: 60518 AN: 151790 Hom.: 13022 Cov.: 33 AF XY: 0.395 AC XY: 29285 AN XY: 74138

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.426

Alfa AF: 0.444 Hom.: 1910

Bravo AF: 0.394

Asia WGS AF: 0.234 AC: 814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.5
DANN	Benign	0.29

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: rs8053806; hg19: chr16-55549397;