chr16-55549638-G-A

Variant names:

• chr16-55549638-G-A
• rs2287072
• NM_017839.5:c.1061+236G>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.1061+236G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 152,080 control chromosomes in the GnomAD database, including 51,540 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 0.80 (51540 hom., cov: 31)
• Consequence: LPCAT2 NM_017839.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.967
• Publications: 3 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LPCAT2	NM_017839.5	c.1061+236G>A		intron_variant	Intron 10 of 13	ENST00000262134.10	NP_060309.2
LPCAT2	XM_047434277.1	c.893+236G>A		intron_variant	Intron 10 of 13		XP_047290233.1
LPCAT2	XM_011523169.4	c.251+236G>A		intron_variant	Intron 7 of 10		XP_011521471.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LPCAT2	ENST00000262134.10	c.1061+236G>A		intron_variant	Intron 10 of 13	1	NM_017839.5	ENSP00000262134.5
LPCAT2	ENST00000566915.5	n.1143+236G>A		intron_variant	Intron 5 of 8	1
LPCAT2	ENST00000563095.5	n.459+236G>A		intron_variant	Intron 2 of 3	3
LPCAT2	ENST00000566375.1	n.97+236G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121353 AN: 151962 Hom.: 51537 Cov.: 31

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.978

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.979

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.940

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.798 AC: 121382 AN: 152080 Hom.: 51540 Cov.: 31 AF XY: 0.800 AC XY: 59460 AN XY: 74348

African (AFR) AF: 0.475 AC: 19689 AN: 41416

American (AMR) AF: 0.875 AC: 13364 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2926 AN: 3472

East Asian (EAS) AF: 0.848 AC: 4382 AN: 5170

South Asian (SAS) AF: 0.809 AC: 3893 AN: 4812

European-Finnish (FIN) AF: 0.979 AC: 10386 AN: 10606

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.940 AC: 63896 AN: 68006

Other (OTH) AF: 0.811 AC: 1717 AN: 2116

Alfa AF: 0.887 Hom.: 190580

Bravo AF: 0.777

Asia WGS AF: 0.762 AC: 2651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.38
DANN	Benign	0.28
PhyloP100		-0.97
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: rs2287072; hg19: chr16-55583550;