rs2279686

Positions:

• chr15-34362517-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_153613.3(LPCAT4):​c.884+56G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 1,495,622 control chromosomes in the GnomAD database, including 186,202 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 0.46 (16449 hom., cov: 32)
  • Exomes 𝑓: 0.50 (169753 hom.)
• Consequence: LPCAT4 NM_153613.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310

Genes affected

LPCAT4 (HGNC:30059): (lysophosphatidylcholine acyltransferase 4) Members of the 1-acylglycerol-3-phosphate O-acyltransferase (EC 2.3.1.51) family, such as AGPAT7, catalyze the conversion of lysophosphatidic acid (LPA) to phosphatidic acid (PA), a precursor in the biosynthesis of all glycerolipids. Both LPA and PA are involved in signal transduction (Ye et al., 2005 [PubMed 16243729]).[supplied by OMIM, May 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LPCAT4	NM_153613.3	c.884+56G>A		intron_variant		ENST00000314891.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LPCAT4	ENST00000314891.11	c.884+56G>A		intron_variant		1	NM_153613.3	P1
LPCAT4	ENST00000567507.1	c.83+56G>A		intron_variant, NMD_transcript_variant		3
LPCAT4	ENST00000563240.1	n.192+56G>A		intron_variant, non_coding_transcript_variant		2
LPCAT4	ENST00000563748.5	n.83+56G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69544 AN: 151888 Hom.: 16441 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.476

GnomAD4 exome AF: 0.500 AC: 671318 AN: 1343614 Hom.: 169753 Cov.: 23 AF XY: 0.498 AC XY: 329244 AN XY: 661026

Gnomad4 AFR exome AF: 0.349

Gnomad4 AMR exome AF: 0.477

Gnomad4 ASJ exome AF: 0.463

Gnomad4 EAS exome AF: 0.307

Gnomad4 SAS exome AF: 0.445

Gnomad4 FIN exome AF: 0.547

Gnomad4 NFE exome AF: 0.514

Gnomad4 OTH exome AF: 0.495

GnomAD4 genome AF: 0.458 AC: 69583 AN: 152008 Hom.: 16449 Cov.: 32 AF XY: 0.458 AC XY: 34024 AN XY: 74316

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.474

Alfa AF: 0.499 Hom.: 27319

Bravo AF: 0.447

Asia WGS AF: 0.356 AC: 1240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.59

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

Publications

LitVar

Other links and lift over

dbSNP: rs2279686; hg19: chr15-34654718; COSMIC: COSV59217801; COSMIC: COSV59217801;