16-55509966-T-C

Variant names:

• chr16-55509966-T-C
• rs12930259
• NM_017839.5:c.171+614T>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.171+614T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 146,996 control chromosomes in the GnomAD database, including 17,113 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 0.47 (17113 hom., cov: 24)
• Consequence: LPCAT2 NM_017839.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.544 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.171+614T>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.171+614T>C		intron	N/A	ENSP00000262134.5
	LPCAT2	ENST00000947554.1		c.171+614T>C		intron	N/A	ENSP00000617613.1
	LPCAT2	ENST00000929287.1		c.171+614T>C		intron	N/A	ENSP00000599346.1

Frequencies

GnomAD3 genomes AF: 0.472 AC: 69385 AN: 146896 Hom.: 17091 Cov.: 24

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.472 AC: 69446 AN: 146996 Hom.: 17113 Cov.: 24 AF XY: 0.466 AC XY: 33212 AN XY: 71234

African (AFR) AF: 0.336 AC: 13376 AN: 39764

American (AMR) AF: 0.524 AC: 7607 AN: 14516

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2077 AN: 3440

East Asian (EAS) AF: 0.315 AC: 1568 AN: 4970

South Asian (SAS) AF: 0.408 AC: 1895 AN: 4644

European-Finnish (FIN) AF: 0.459 AC: 4226 AN: 9216

Middle Eastern (MID) AF: 0.511 AC: 143 AN: 280

European-Non Finnish (NFE) AF: 0.549 AC: 36882 AN: 67220

Other (OTH) AF: 0.517 AC: 1058 AN: 2048

Alfa AF: 0.514 Hom.: 2457

Bravo AF: 0.478

Asia WGS AF: 0.374 AC: 1299 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.59
PhyloP100		-0.39
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: rs12930259; hg19: chr16-55543878;