rs7162607

chr15-34358785-G-Achr15-34358785-G-C

Variant summary

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

The NM_153613.3(LPCAT4):c.*342C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 154,470 control chromosomes in the GnomAD database, including 18,832 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 0.49 (18578 hom., cov: 31)
  • Exomes 𝑓: 0.44 (254 hom.)
• Consequence: LPCAT4 NM_153613.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.694

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LPCAT4	NM_153613.3	c.*342C>T		3_prime_UTR_variant	14/14	ENST00000314891.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LPCAT4	ENST00000314891.11	c.*342C>T		3_prime_UTR_variant	14/14	1	NM_153613.3	P1

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74592 AN: 151826 Hom.: 18563 Cov.: 31

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.460

GnomAD4 exome AF: 0.438 AC: 1107 AN: 2526 Hom.: 254 Cov.: 0 AF XY: 0.430 AC XY: 708 AN XY: 1648

Gnomad4 AFR exome AF: 0.778

Gnomad4 AMR exome AF: 0.538

Gnomad4 ASJ exome AF: 0.357

Gnomad4 EAS exome AF: 0.418

Gnomad4 SAS exome AF: 0.375

Gnomad4 FIN exome AF: 0.462

Gnomad4 NFE exome AF: 0.425

Gnomad4 OTH exome AF: 0.456

GnomAD4 genome AF: 0.491 AC: 74662 AN: 151944 Hom.: 18578 Cov.: 31 AF XY: 0.490 AC XY: 36353 AN XY: 74234

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.460

Alfa AF: 0.462 Hom.: 9907

Bravo AF: 0.503

Asia WGS AF: 0.478 AC: 1662 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	3.4
Dann	Benign	0.48

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: rs7162607; hg19: chr15-34650986; COSMIC: COSV59217795; COSMIC: COSV59217795;