chr16-55569556-C-T

Variant names:

• chr16-55569556-C-T
• rs168822
• NM_017839.5:c.1216-5075C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017839.5(LPCAT2):​c.1216-5075C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,056 control chromosomes in the GnomAD database, including 12,382 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 0.38 (12382 hom., cov: 33)
• Consequence: LPCAT2 NM_017839.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.566
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017839.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPCAT2	NM_017839.5	MANE Select	c.1216-5075C>T		intron	N/A	NP_060309.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPCAT2	ENST00000262134.10	TSL:1 MANE Select	c.1216-5075C>T		intron	N/A	ENSP00000262134.5
	LPCAT2	ENST00000566915.5	TSL:1	n.1298-5075C>T		intron	N/A
	LPCAT2	ENST00000563095.5	TSL:3	n.614-5075C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58356 AN: 151938 Hom.: 12378 Cov.: 33

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.384 AC: 58383 AN: 152056 Hom.: 12382 Cov.: 33 AF XY: 0.381 AC XY: 28340 AN XY: 74322

African (AFR) AF: 0.204 AC: 8459 AN: 41474

American (AMR) AF: 0.446 AC: 6819 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1740 AN: 3468

East Asian (EAS) AF: 0.263 AC: 1362 AN: 5172

South Asian (SAS) AF: 0.288 AC: 1391 AN: 4822

European-Finnish (FIN) AF: 0.477 AC: 5035 AN: 10562

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32109 AN: 67954

Other (OTH) AF: 0.396 AC: 838 AN: 2116

Alfa AF: 0.448 Hom.: 15141

Bravo AF: 0.375

Asia WGS AF: 0.224 AC: 779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.84
DANN	Benign	0.59
PhyloP100		-0.57
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs168822; hg19: chr16-55603468;