dbSNP rs2279686: LPCAT4:c.884+56G>A (chr15-34362517-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.310

Publications

19 publications found

Variant links:

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]

LPCAT4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LPCAT4	NM_153613.3 link	c.884+56G>A		intron_variant	Intron 9 of 13	ENST00000314891.11	NP_705841.2	Q643R3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LPCAT4	ENST00000314891.11 link	c.884+56G>A		intron_variant	Intron 9 of 13	1	NM_153613.3	ENSP00000317300.6		Q643R3

Frequencies

GnomAD3 genomes

AF:

0.458

AC:

69544

AN:

151888

Hom.:

16441

Cov.:

show subpopulations

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.:

AF XY:

0.498

AC XY:

329244

AN XY:

661026

show subpopulations

African (AFR)

AF:

0.349

AC:

10517

AN:

30138

American (AMR)

AF:

0.477

AC:

15480

AN:

32446

Ashkenazi Jewish (ASJ)

AF:

0.463

AC:

9405

AN:

20324

East Asian (EAS)

AF:

0.307

AC:

11908

AN:

38806

South Asian (SAS)

AF:

0.445

AC:

31833

AN:

71562

European-Finnish (FIN)

AF:

0.547

AC:

27304

AN:

49894

Middle Eastern (MID)

AF:

0.525

AC:

2655

AN:

5058

European-Non Finnish (NFE)

AF:

0.514

AC:

534720

AN:

1039830

Other (OTH)

AF:

0.495

AC:

27496

AN:

55556

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

16902

33804

50706

67608

84510

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15682

31364

47046

62728

78410

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.458

AC:

69583

AN:

152008

Hom.:

16449

Cov.:

AF XY:

0.458

AC XY:

34024

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.361

AC:

14953

AN:

41432

American (AMR)

AF:

0.470

AC:

7188

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.458

AC:

1590

AN:

3472

East Asian (EAS)

AF:

0.308

AC:

1592

AN:

5172

South Asian (SAS)

AF:

0.415

AC:

2005

AN:

4826

European-Finnish (FIN)

AF:

0.556

AC:

5864

AN:

10546

Middle Eastern (MID)

AF:

0.551

AC:

162

AN:

294

European-Non Finnish (NFE)

AF:

0.510

AC:

34692

AN:

67974

Other (OTH)

AF:

0.474

AC:

996

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1883

3765

5648

7530

9413

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

648

1296

1944

2592

3240

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.496

Hom.:

43037

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

(source)

DANN

Benign

0.59

PhyloP100

-0.31

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over