ENST00000566915.5:n.1834C>T

Variant names:

• chr16-55583215-C-T
• rs12934747
• ENST00000566915.5:n.1834C>T

Variant summary

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

The ENST00000566915.5(LPCAT2):​n.1834C>T variant causes a non coding transcript exon 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 ENST00000566915.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 15 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]

ENSG00000294394 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000566915.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPCAT2	NM_017839.5	MANE Select	c.*117C>T		3_prime_UTR	Exon 14 of 14	NP_060309.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPCAT2	ENST00000566915.5	TSL:1	n.1834C>T		non_coding_transcript_exon	Exon 9 of 9
	LPCAT2	ENST00000262134.10	TSL:1 MANE Select	c.*117C>T		3_prime_UTR	Exon 14 of 14	ENSP00000262134.5
	LPCAT2	ENST00000562299.1	TSL:2	n.529C>T		non_coding_transcript_exon	Exon 2 of 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

African (AFR) AF: 0.601 AC: 9737 AN: 16196

American (AMR) AF: 0.496 AC: 7960 AN: 16052

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 5668 AN: 13440

East Asian (EAS) AF: 0.702 AC: 21789 AN: 31058

South Asian (SAS) AF: 0.618 AC: 17160 AN: 27780

European-Finnish (FIN) AF: 0.519 AC: 19190 AN: 36972

Middle Eastern (MID) AF: 0.478 AC: 1698 AN: 3556

European-Non Finnish (NFE) AF: 0.497 AC: 227903 AN: 458804

Other (OTH) AF: 0.522 AC: 15960 AN: 30594

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

African (AFR) AF: 0.596 AC: 24720 AN: 41464

American (AMR) AF: 0.495 AC: 7556 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1426 AN: 3470

East Asian (EAS) AF: 0.728 AC: 3764 AN: 5168

South Asian (SAS) AF: 0.641 AC: 3088 AN: 4816

European-Finnish (FIN) AF: 0.527 AC: 5555 AN: 10546

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33906 AN: 67936

Other (OTH) AF: 0.532 AC: 1123 AN: 2110

Alfa AF: 0.517 Hom.: 4971

Bravo AF: 0.537

Asia WGS AF: 0.731 AC: 2540 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.18
DANN	Benign	0.41
PhyloP100		-0.27
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: rs12934747; hg19: chr16-55617127;