Genetic Variant AGPAT4:c.348+440G>A (chr6-161165808-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_020133.3(AGPAT4):c.348+440G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 582,546 control chromosomes in the GnomAD database, including 8,097 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 0.15 ( 2089 hom., cov: 32)

Exomes 𝑓: 0.14 ( 6008 hom. )

Consequence

AGPAT4
NM_020133.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.67

Publications

2 publications found

Variant links:

Genes affected

AGPAT4 (HGNC:20885): (1-acylglycerol-3-phosphate O-acyltransferase 4) This gene encodes a member of the 1-acylglycerol-3-phosphate O-acyltransferase family. This integral membrane protein converts lysophosphatidic acid to phosphatidic acid, the second step in de novo phospholipid biosynthesis. [provided by RefSeq, Jul 2008]

AGPAT4 links:

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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=-0.97).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020133.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AGPAT4	NM_020133.3	MANE Select	c.348+440G>A		intron	N/A	NP_064518.1	Q9NRZ5-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
AGPAT4	ENST00000320285.9	TSL:1 MANE Select	c.348+440G>A	intron	N/A	ENSP00000314036.4	Q9NRZ5-1
AGPAT4	ENST00000436279.1	TSL:1	n.349-95G>A	intron	N/A	ENSP00000413901.1	G3XAF1
AGPAT4	ENST00000860938.1		c.348+440G>A	intron	N/A	ENSP00000530997.1

Frequencies

GnomAD3 genomes

AF:

0.146

AC:

22106

AN:

151830

Hom.:

2081

Cov.:

show subpopulations

Gnomad AFR

AF:

0.188

Gnomad AMI

AF:

0.190

Gnomad AMR

AF:

0.275

Gnomad ASJ

AF:

0.0880

Gnomad EAS

AF:

0.263

Gnomad SAS

AF:

0.244

Gnomad FIN

AF:

0.0492

Gnomad MID

AF:

0.158

Gnomad NFE

AF:

0.0918

Gnomad OTH

AF:

0.148

GnomAD4 exome

AF:

0.140

AC:

60129

AN:

430610

Hom.:

6008

Cov.:

AF XY:

0.143

AC XY:

33763

AN XY:

235992

show subpopulations

African (AFR)

AF:

0.190

AC:

2378

AN:

12516

American (AMR)

AF:

0.366

AC:

10423

AN:

28506

Ashkenazi Jewish (ASJ)

AF:

0.0807

AC:

1237

AN:

15334

East Asian (EAS)

AF:

0.254

AC:

4994

AN:

19686

South Asian (SAS)

AF:

0.235

AC:

13831

AN:

58870

European-Finnish (FIN)

AF:

0.0537

AC:

1215

AN:

22644

Middle Eastern (MID)

AF:

0.156

AC:

270

AN:

1736

European-Non Finnish (NFE)

AF:

0.0917

AC:

22804

AN:

248572

Other (OTH)

AF:

0.131

AC:

2977

AN:

22746

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

2492

4984

7477

9969

12461

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

364

728

1092

1456

1820

<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:

0.146

AC:

22146

AN:

151936

Hom.:

2089

Cov.:

AF XY:

0.148

AC XY:

11018

AN XY:

74218

show subpopulations

African (AFR)

AF:

0.189

AC:

7812

AN:

41442

American (AMR)

AF:

0.275

AC:

4201

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.0880

AC:

305

AN:

3466

East Asian (EAS)

AF:

0.263

AC:

1360

AN:

5162

South Asian (SAS)

AF:

0.244

AC:

1174

AN:

4816

European-Finnish (FIN)

AF:

0.0492

AC:

517

AN:

10500

Middle Eastern (MID)

AF:

0.168

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0918

AC:

6240

AN:

67984

Other (OTH)

AF:

0.149

AC:

315

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

924

1848

2772

3696

4620

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

234

468

702

936

1170

<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:

0.115

Hom.:

3935

Bravo

AF:

0.166

Asia WGS

AF:

0.249

AC:

867

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.094

(source)

DANN

Benign

0.39

PhyloP100

-1.7

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