dbSNP rs10521319: LPCAT2:c.853-211A>C (chr16-55545524-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_017839.5(LPCAT2):c.853-211A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0724 in 398,670 control chromosomes in the GnomAD database, including 1,575 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 0.089 ( 874 hom., cov: 32)

Exomes 𝑓: 0.062 ( 701 hom. )

Consequence

LPCAT2
NM_017839.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.228

Publications

4 publications found

Variant links:

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 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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
LPCAT2	NM_017839.5 link	c.853-211A>C	intron_variant	Intron 8 of 13	ENST00000262134.10	NP_060309.2	Q7L5N7-1
LPCAT2	XM_047434277.1 link	c.685-211A>C	intron_variant	Intron 8 of 13		XP_047290233.1
LPCAT2	XM_011523169.4 link	c.43-211A>C	intron_variant	Intron 5 of 10		XP_011521471.1	Q7L5N7-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
LPCAT2	ENST00000262134.10 link	c.853-211A>C	intron_variant	Intron 8 of 13	1	NM_017839.5	ENSP00000262134.5	Q7L5N7-1
LPCAT2	ENST00000566915.5 link	n.935-211A>C	intron_variant	Intron 3 of 8	1
LPCAT2	ENST00000563095.5 link	n.40A>C	non_coding_transcript_exon_variant	Exon 1 of 4	3

Frequencies

GnomAD3 genomes

AF:

0.0888

AC:

13493

AN:

152012

Hom.:

862

Cov.:

show subpopulations

Gnomad AFR

AF:

0.173

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.0587

Gnomad ASJ

AF:

0.0694

Gnomad EAS

AF:

0.144

Gnomad SAS

AF:

0.127

Gnomad FIN

AF:

0.0196

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.0500

Gnomad OTH

AF:

0.0947

GnomAD4 exome

AF:

0.0622

AC:

15341

AN:

246540

Hom.:

701

Cov.:

AF XY:

0.0622

AC XY:

7884

AN XY:

126672

show subpopulations

African (AFR)

AF:

0.173

AC:

1168

AN:

6750

American (AMR)

AF:

0.0631

AC:

467

AN:

7406

Ashkenazi Jewish (ASJ)

AF:

0.0619

AC:

531

AN:

8578

East Asian (EAS)

AF:

0.137

AC:

2831

AN:

20712

South Asian (SAS)

AF:

0.115

AC:

915

AN:

7954

European-Finnish (FIN)

AF:

0.0214

AC:

539

AN:

25222

Middle Eastern (MID)

AF:

0.0855

AC:

103

AN:

1204

European-Non Finnish (NFE)

AF:

0.0496

AC:

7608

AN:

153244

Other (OTH)

AF:

0.0762

AC:

1179

AN:

15470

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

656

1312

1967

2623

3279

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

132

198

264

330

<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:

0.0890

AC:

13540

AN:

152130

Hom.:

874

Cov.:

AF XY:

0.0882

AC XY:

6559

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.173

AC:

7179

AN:

41468

American (AMR)

AF:

0.0586

AC:

895

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.0694

AC:

241

AN:

3472

East Asian (EAS)

AF:

0.144

AC:

743

AN:

5162

South Asian (SAS)

AF:

0.128

AC:

616

AN:

4818

European-Finnish (FIN)

AF:

0.0196

AC:

208

AN:

10604

Middle Eastern (MID)

AF:

0.116

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0500

AC:

3398

AN:

68010

Other (OTH)

AF:

0.103

AC:

217

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

591

1181

1772

2362

2953

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

158

316

474

632

790

<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:

0.0651

Hom.:

249

Bravo

AF:

0.0980

Asia WGS

AF:

0.184

AC:

638

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.3

(source)

DANN

Benign

0.77

PhyloP100

0.23

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