16-55579006-T-G

Variant names:

• chr16-55579006-T-G
• rs4784549
• NM_017839.5:c.1315-103T>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_017839.5(LPCAT2):​c.1315-103T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LPCAT2 NM_017839.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.70
• Publications: 10 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LPCAT2	NM_017839.5	c.1315-103T>G		intron_variant	Intron 12 of 13	ENST00000262134.10	NP_060309.2
LPCAT2	XM_047434277.1	c.1147-103T>G		intron_variant	Intron 12 of 13		XP_047290233.1
LPCAT2	XM_011523169.4	c.505-103T>G		intron_variant	Intron 9 of 10		XP_011521471.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LPCAT2	ENST00000262134.10	c.1315-103T>G		intron_variant	Intron 12 of 13	1	NM_017839.5	ENSP00000262134.5
LPCAT2	ENST00000566915.5	n.1397-103T>G		intron_variant	Intron 7 of 8	1
LPCAT2	ENST00000565056.1	n.189-103T>G		intron_variant	Intron 2 of 3	3
LPCAT2	ENST00000562299.1	n.-12T>G		upstream_gene_variant		2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 903940 Hom.: 0 Cov.: 12 AF XY: 0.00 AC XY: 0 AN XY: 463438

African (AFR) AF: 0.00 AC: 0 AN: 21344

American (AMR) AF: 0.00 AC: 0 AN: 32306

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17854

East Asian (EAS) AF: 0.00 AC: 0 AN: 36856

South Asian (SAS) AF: 0.00 AC: 0 AN: 61856

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47662

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2916

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 642146

Other (OTH) AF: 0.00 AC: 0 AN: 41000

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.046
DANN	Benign	0.36
PhyloP100		-2.7

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: rs4784549; hg19: chr16-55612918;