chr16-55515948-G-C

Variant names:

• chr16-55515948-G-C
• rs12708952
• NM_017839.5:c.171+6596G>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+6596G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,956 control chromosomes in the GnomAD database, including 20,485 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 0.52 (20485 hom., cov: 33)
• Consequence: LPCAT2 NM_017839.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 6 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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.547 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.171+6596G>C		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.171+6596G>C		intron	N/A	ENSP00000262134.5
	LPCAT2	ENST00000566911.1	TSL:2	n.281+6596G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78393 AN: 151838 Hom.: 20457 Cov.: 33

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.516 AC: 78467 AN: 151956 Hom.: 20485 Cov.: 33 AF XY: 0.513 AC XY: 38084 AN XY: 74274

African (AFR) AF: 0.465 AC: 19281 AN: 41450

American (AMR) AF: 0.550 AC: 8401 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2232 AN: 3466

East Asian (EAS) AF: 0.348 AC: 1802 AN: 5174

South Asian (SAS) AF: 0.467 AC: 2252 AN: 4822

European-Finnish (FIN) AF: 0.481 AC: 5074 AN: 10538

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.552 AC: 37491 AN: 67926

Other (OTH) AF: 0.547 AC: 1155 AN: 2112

Alfa AF: 0.416 Hom.: 1116

Bravo AF: 0.520

Asia WGS AF: 0.428 AC: 1485 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.36
PhyloP100		-0.93
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: rs12708952; hg19: chr16-55549860;