NM_017839.5:c.1315-103T>A

Variant names:

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

Variant summary

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

The NM_017839.5(LPCAT2):​c.1315-103T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 1,053,600 control chromosomes in the GnomAD database, including 165,492 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 0.61 (29231 hom., cov: 32)
  • Exomes 𝑓: 0.54 (136261 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LPCAT2	NM_017839.5	c.1315-103T>A		intron_variant	Intron 12 of 13	ENST00000262134.10	NP_060309.2
LPCAT2	XM_047434277.1	c.1147-103T>A		intron_variant	Intron 12 of 13		XP_047290233.1
LPCAT2	XM_011523169.4	c.505-103T>A		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>A		intron_variant	Intron 12 of 13	1	NM_017839.5	ENSP00000262134.5
LPCAT2	ENST00000566915.5	n.1397-103T>A		intron_variant	Intron 7 of 8	1
LPCAT2	ENST00000565056.1	n.189-103T>A		intron_variant	Intron 2 of 3	3
LPCAT2	ENST00000562299.1	n.-12T>A		upstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92111 AN: 152002 Hom.: 29194 Cov.: 32

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.584

GnomAD4 exome AF: 0.543 AC: 489942 AN: 901480 Hom.: 136261 Cov.: 12 AF XY: 0.547 AC XY: 253023 AN XY: 462238

African (AFR) AF: 0.805 AC: 17156 AN: 21300

American (AMR) AF: 0.559 AC: 18026 AN: 32244

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 8689 AN: 17814

East Asian (EAS) AF: 0.719 AC: 26479 AN: 36814

South Asian (SAS) AF: 0.687 AC: 42431 AN: 61784

European-Finnish (FIN) AF: 0.521 AC: 24804 AN: 47578

Middle Eastern (MID) AF: 0.579 AC: 1686 AN: 2912

European-Non Finnish (NFE) AF: 0.512 AC: 327802 AN: 640146

Other (OTH) AF: 0.559 AC: 22869 AN: 40888

GnomAD4 genome AF: 0.606 AC: 92203 AN: 152120 Hom.: 29231 Cov.: 32 AF XY: 0.609 AC XY: 45302 AN XY: 74360

African (AFR) AF: 0.793 AC: 32929 AN: 41524

American (AMR) AF: 0.545 AC: 8317 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1680 AN: 3468

East Asian (EAS) AF: 0.736 AC: 3804 AN: 5170

South Asian (SAS) AF: 0.710 AC: 3428 AN: 4826

European-Finnish (FIN) AF: 0.519 AC: 5487 AN: 10574

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34865 AN: 67980

Other (OTH) AF: 0.589 AC: 1245 AN: 2112

Alfa AF: 0.559 Hom.: 3019

Bravo AF: 0.614

Asia WGS AF: 0.775 AC: 2698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.045
DANN	Benign	0.55
PhyloP100		-2.7
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: rs4784549; hg19: chr16-55612918; COSMIC: COSV50896865; COSMIC: COSV50896865;