rs10521319

Variant names:

• chr16-55545524-A-C
• rs10521319
• NM_017839.5:c.853-211A>C

Variant summary

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

The NM_017839.5(LPCAT2):​c.853-211A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0724 in 398,670 control chromosomes in the GnomAD database, including 1,575 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 0.089 (874 hom., cov: 32)
  • Exomes 𝑓: 0.062 (701 hom.)
• Consequence: LPCAT2 NM_017839.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 4 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.17 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPCAT2	NM_017839.5	MANE Select	c.853-211A>C		intron	N/A	NP_060309.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPCAT2	ENST00000262134.10	TSL:1 MANE Select	c.853-211A>C		intron	N/A	ENSP00000262134.5	Q7L5N7-1
	LPCAT2	ENST00000566915.5	TSL:1	n.935-211A>C		intron	N/A
	LPCAT2	ENST00000947554.1		c.874-211A>C		intron	N/A	ENSP00000617613.1

Frequencies

GnomAD3 genomes AF: 0.0888 AC: 13493 AN: 152012 Hom.: 862 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0587

Gnomad ASJ AF: 0.0694

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0196

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0500

Gnomad OTH AF: 0.0947

GnomAD4 exome AF: 0.0622 AC: 15341 AN: 246540 Hom.: 701 Cov.: 2 AF XY: 0.0622 AC XY: 7884 AN XY: 126672

African (AFR) AF: 0.173 AC: 1168 AN: 6750

American (AMR) AF: 0.0631 AC: 467 AN: 7406

Ashkenazi Jewish (ASJ) AF: 0.0619 AC: 531 AN: 8578

East Asian (EAS) AF: 0.137 AC: 2831 AN: 20712

South Asian (SAS) AF: 0.115 AC: 915 AN: 7954

European-Finnish (FIN) AF: 0.0214 AC: 539 AN: 25222

Middle Eastern (MID) AF: 0.0855 AC: 103 AN: 1204

European-Non Finnish (NFE) AF: 0.0496 AC: 7608 AN: 153244

Other (OTH) AF: 0.0762 AC: 1179 AN: 15470

GnomAD4 genome AF: 0.0890 AC: 13540 AN: 152130 Hom.: 874 Cov.: 32 AF XY: 0.0882 AC XY: 6559 AN XY: 74376

African (AFR) AF: 0.173 AC: 7179 AN: 41468

American (AMR) AF: 0.0586 AC: 895 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0694 AC: 241 AN: 3472

East Asian (EAS) AF: 0.144 AC: 743 AN: 5162

South Asian (SAS) AF: 0.128 AC: 616 AN: 4818

European-Finnish (FIN) AF: 0.0196 AC: 208 AN: 10604

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 292

European-Non Finnish (NFE) AF: 0.0500 AC: 3398 AN: 68010

Other (OTH) AF: 0.103 AC: 217 AN: 2112

Alfa AF: 0.0651 Hom.: 249

Bravo AF: 0.0980

Asia WGS AF: 0.184 AC: 638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.3
DANN	Benign	0.77
PhyloP100		0.23
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10521319;

hg19: chr16-55579436;