16-55575346-G-A

Variant names:

• chr16-55575346-G-A
• rs183154
• NM_017839.5:c.1314+617G>A

Variant summary

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

The NM_017839.5(LPCAT2):​c.1314+617G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.951 in 152,224 control chromosomes in the GnomAD database, including 69,037 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 0.95 (69037 hom., cov: 32)
• Consequence: LPCAT2 NM_017839.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556
• Publications: 1 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.984 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.1314+617G>A		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.1314+617G>A		intron	N/A	ENSP00000262134.5
	LPCAT2	ENST00000566915.5	TSL:1	n.1396+617G>A		intron	N/A
	LPCAT2	ENST00000565056.1	TSL:3	n.188+617G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.951 AC: 144629 AN: 152106 Hom.: 68989 Cov.: 32

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.959

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.940

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.958

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

GnomAD4 genome AF: 0.951 AC: 144735 AN: 152224 Hom.: 69037 Cov.: 32 AF XY: 0.950 AC XY: 70732 AN XY: 74438

African (AFR) AF: 0.866 AC: 35921 AN: 41496

American (AMR) AF: 0.959 AC: 14664 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3288 AN: 3470

East Asian (EAS) AF: 0.992 AC: 5132 AN: 5174

South Asian (SAS) AF: 0.940 AC: 4533 AN: 4822

European-Finnish (FIN) AF: 0.999 AC: 10611 AN: 10620

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.990 AC: 67383 AN: 68036

Other (OTH) AF: 0.958 AC: 2028 AN: 2116

Alfa AF: 0.976 Hom.: 33094

Bravo AF: 0.946

Asia WGS AF: 0.962 AC: 3345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.073
DANN	Benign	0.18
PhyloP100		-0.56
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: rs183154; hg19: chr16-55609258;