dbSNP rs7162607: LPCAT4:c.*342C>T (chr15-34358785-G-A) – 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.*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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.694

Publications

5 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=-0.88).

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 rank	MANE	Protein	UniProt
LPCAT4	NM_153613.3 link	c.*342C>T		3_prime_UTR_variant	Exon 14 of 14	ENST00000314891.11	NP_705841.2	Q643R3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LPCAT4	ENST00000314891.11 link	c.*342C>T		3_prime_UTR_variant	Exon 14 of 14	1	NM_153613.3	ENSP00000317300.6		Q643R3
LPCAT4	ENST00000563748.5 link	n.*124C>T		downstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.491

AC:

74592

AN:

151826

Hom.:

18563

Cov.:

show subpopulations

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.:

AF XY:

0.430

AC XY:

708

AN XY:

1648

show subpopulations

African (AFR)

AF:

0.778

AC:

AN:

American (AMR)

AF:

0.538

AC:

AN:

106

Ashkenazi Jewish (ASJ)

AF:

0.357

AC:

AN:

East Asian (EAS)

AF:

0.418

AC:

AN:

110

South Asian (SAS)

AF:

0.375

AC:

AN:

112

European-Finnish (FIN)

AF:

0.462

AC:

205

AN:

444

Middle Eastern (MID)

AF:

0.167

AC:

AN:

European-Non Finnish (NFE)

AF:

0.425

AC:

687

AN:

1616

Other (OTH)

AF:

0.456

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

122

153

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.491

AC:

74662

AN:

151944

Hom.:

18578

Cov.:

AF XY:

0.490

AC XY:

36353

AN XY:

74234

show subpopulations

African (AFR)

AF:

0.574

AC:

23795

AN:

41452

American (AMR)

AF:

0.530

AC:

8086

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.459

AC:

1592

AN:

3470

East Asian (EAS)

AF:

0.504

AC:

2604

AN:

5162

South Asian (SAS)

AF:

0.457

AC:

2203

AN:

4822

European-Finnish (FIN)

AF:

0.427

AC:

4488

AN:

10518

Middle Eastern (MID)

AF:

0.483

AC:

141

AN:

292

European-Non Finnish (NFE)

AF:

0.445

AC:

30217

AN:

67940

Other (OTH)

AF:

0.460

AC:

971

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

1895

3790

5686

7581

9476

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

664

1328

1992

2656

3320

<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:

0.464

Hom.:

18953

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

(source)

DANN

Benign

0.48

PhyloP100

0.69

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