16-55570216-A-T

Variant names:

• chr16-55570216-A-T
• rs6499766
• NM_017839.5:c.1216-4415A>T

Variant summary

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

The NM_017839.5(LPCAT2):​c.1216-4415A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 152,012 control chromosomes in the GnomAD database, including 23,161 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 0.55 (23161 hom., cov: 33)
• Consequence: LPCAT2 NM_017839.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• Publications: 19 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 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.1216-4415A>T		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.1216-4415A>T		intron	N/A	ENSP00000262134.5	Q7L5N7-1
	LPCAT2	ENST00000566915.5	TSL:1	n.1298-4415A>T		intron	N/A
	LPCAT2	ENST00000947554.1		c.1237-4415A>T		intron	N/A	ENSP00000617613.1

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83044 AN: 151894 Hom.: 23142 Cov.: 33

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.547 AC: 83110 AN: 152012 Hom.: 23161 Cov.: 33 AF XY: 0.550 AC XY: 40842 AN XY: 74322

African (AFR) AF: 0.625 AC: 25876 AN: 41428

American (AMR) AF: 0.499 AC: 7615 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1496 AN: 3468

East Asian (EAS) AF: 0.728 AC: 3765 AN: 5170

South Asian (SAS) AF: 0.650 AC: 3139 AN: 4830

European-Finnish (FIN) AF: 0.517 AC: 5469 AN: 10572

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.503 AC: 34187 AN: 67956

Other (OTH) AF: 0.542 AC: 1145 AN: 2112

Alfa AF: 0.517 Hom.: 2516

Bravo AF: 0.549

Asia WGS AF: 0.736 AC: 2561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.72
PhyloP100		-0.095
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: rs6499766; hg19: chr16-55604128;