rs12934747

Positions:

• chr16-55583215-C-T

Variant summary

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

The NM_017839.5(LPCAT2):​c.*117C>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 0.52 in 786,426 control chromosomes in the GnomAD database, including 108,152 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 0.54 (22259 hom., cov: 33)
  • Exomes 𝑓: 0.52 (85893 hom.)
• Consequence: LPCAT2 NM_017839.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271

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]

LPCAT2 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LPCAT2	NM_017839.5	c.*117C>T		3_prime_UTR_variant	14/14	ENST00000262134.10	NP_060309.2
LPCAT2	XM_047434277.1	c.*117C>T		3_prime_UTR_variant	14/14		XP_047290233.1
LPCAT2	XM_011523169.4	c.*117C>T		3_prime_UTR_variant	11/11		XP_011521471.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LPCAT2	ENST00000262134.10	c.*117C>T		3_prime_UTR_variant	14/14	1	NM_017839.5	ENSP00000262134.5
LPCAT2	ENST00000566915.5	n.1834C>T		non_coding_transcript_exon_variant	9/9	1
LPCAT2	ENST00000562299.1	n.529C>T		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81486 AN: 151856 Hom.: 22239 Cov.: 33

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.526

GnomAD4 exome AF: 0.516 AC: 327065 AN: 634452 Hom.: 85893 Cov.: 9 AF XY: 0.517 AC XY: 164032 AN XY: 317396

Gnomad4 AFR exome AF: 0.601

Gnomad4 AMR exome AF: 0.496

Gnomad4 ASJ exome AF: 0.422

Gnomad4 EAS exome AF: 0.702

Gnomad4 SAS exome AF: 0.618

Gnomad4 FIN exome AF: 0.519

Gnomad4 NFE exome AF: 0.497

Gnomad4 OTH exome AF: 0.522

GnomAD4 genome AF: 0.537 AC: 81552 AN: 151974 Hom.: 22259 Cov.: 33 AF XY: 0.539 AC XY: 40067 AN XY: 74286

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.728

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.532

Alfa AF: 0.514 Hom.: 4322

Bravo AF: 0.537

Asia WGS AF: 0.731 AC: 2540 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.18
DANN	Benign	0.41

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: rs12934747; hg19: chr16-55617127;