dbSNP rs11786297: GPAT4:c.1262+495A>G (chr8-41619472-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_178819.4(GPAT4):c.1262+495A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0781 in 173,204 control chromosomes in the GnomAD database, including 602 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 0.080 ( 550 hom., cov: 33)

Exomes 𝑓: 0.061 ( 52 hom. )

Consequence

GPAT4
NM_178819.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.131

Publications

4 publications found

Variant links:

Genes affected

GPAT4 (HGNC:20880): (glycerol-3-phosphate acyltransferase 4) Lysophosphatidic acid acyltransferases (EC 2.3.1.51) catalyze the conversion of lysophosphatidic acid (LPA) to phosphatidic acid (PA). LPA and PA are involved in signal transduction and lipid biosynthesis.[supplied by OMIM, Apr 2004]

GPAT4 links:

ENSG00000264578 (HGNC:):

ENSG00000264578 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 (AMR) allele frequency at 95% confidence interval = 0.0876 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178819.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GPAT4	NM_178819.4	MANE Select	c.1262+495A>G	intron	N/A	NP_848934.1	Q86UL3
GPAT4	NM_001363197.2		c.1262+495A>G	intron	N/A	NP_001350126.1	Q86UL3
GPAT4	NM_001363198.2		c.638+495A>G	intron	N/A	NP_001350127.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GPAT4	ENST00000396987.7	TSL:1 MANE Select	c.1262+495A>G	intron	N/A	ENSP00000380184.3	Q86UL3
GPAT4	ENST00000863294.1		c.1262+495A>G	intron	N/A	ENSP00000533353.1
GPAT4	ENST00000863297.1		c.1262+495A>G	intron	N/A	ENSP00000533356.1

Frequencies

GnomAD3 genomes

AF:

0.0805

AC:

12244

AN:

152142

Hom.:

549

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0901

Gnomad AMI

AF:

0.0341

Gnomad AMR

AF:

0.0909

Gnomad ASJ

AF:

0.124

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.0455

Gnomad FIN

AF:

0.0402

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.0845

Gnomad OTH

AF:

0.104

GnomAD4 exome

AF:

0.0606

AC:

1269

AN:

20944

Hom.:

AF XY:

0.0612

AC XY:

662

AN XY:

10822

show subpopulations

African (AFR)

AF:

0.100

AC:

AN:

518

American (AMR)

AF:

0.0640

AC:

202

AN:

3156

Ashkenazi Jewish (ASJ)

AF:

0.0710

AC:

AN:

324

East Asian (EAS)

AF:

0.00

AC:

AN:

1494

South Asian (SAS)

AF:

0.0373

AC:

AN:

2522

European-Finnish (FIN)

AF:

0.0289

AC:

AN:

554

Middle Eastern (MID)

AF:

0.118

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0712

AC:

811

AN:

11390

Other (OTH)

AF:

0.0704

AC:

AN:

952

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

112

167

223

279

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.0805

AC:

12250

AN:

152260

Hom.:

550

Cov.:

AF XY:

0.0790

AC XY:

5881

AN XY:

74452

show subpopulations

African (AFR)

AF:

0.0901

AC:

3740

AN:

41532

American (AMR)

AF:

0.0907

AC:

1387

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.124

AC:

431

AN:

3472

East Asian (EAS)

AF:

0.000578

AC:

AN:

5188

South Asian (SAS)

AF:

0.0460

AC:

222

AN:

4826

European-Finnish (FIN)

AF:

0.0402

AC:

427

AN:

10622

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0846

AC:

5751

AN:

68014

Other (OTH)

AF:

0.103

AC:

217

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

583

1165

1748

2330

2913

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

264

396

528

660

<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:

0.0846

Hom.:

713

Bravo

AF:

0.0841

Asia WGS

AF:

0.0210

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.4

(source)

DANN

Benign

0.26

PhyloP100

0.13

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over