dbSNP rs6934457: AGPAT4:c.348+4745A>G (chr6-161161503-T-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_020133.3(AGPAT4):c.348+4745A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 456,512 control chromosomes in the GnomAD database, including 17,591 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 0.31 ( 9752 hom., cov: 33)

Exomes 𝑓: 0.21 ( 7839 hom. )

Consequence

AGPAT4
NM_020133.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.03

Publications

8 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:

AGPAT4-IT1 (HGNC:20988): (AGPAT4 intronic transcript 1)

AGPAT4-IT1 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=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.582 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+4745A>G		intron	N/A	NP_064518.1	Q9NRZ5-1
	AGPAT4-IT1	NR_024277.1		n.480A>G		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
AGPAT4	ENST00000320285.9	TSL:1 MANE Select	c.348+4745A>G	intron	N/A	ENSP00000314036.4	Q9NRZ5-1
AGPAT4	ENST00000436279.1	TSL:1	n.*83+4074A>G	intron	N/A	ENSP00000413901.1	G3XAF1
AGPAT4	ENST00000860938.1		c.348+4745A>G	intron	N/A	ENSP00000530997.1

Frequencies

GnomAD3 genomes

AF:

0.312

AC:

47454

AN:

152008

Hom.:

9720

Cov.:

show subpopulations

Gnomad AFR

AF:

0.587

Gnomad AMI

AF:

0.164

Gnomad AMR

AF:

0.205

Gnomad ASJ

AF:

0.217

Gnomad EAS

AF:

0.0378

Gnomad SAS

AF:

0.179

Gnomad FIN

AF:

0.249

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.217

Gnomad OTH

AF:

0.298

GnomAD2 exomes

AF:

0.205

AC:

28036

AN:

136620

AF XY:

0.202

show subpopulations

Gnomad AFR exome

AF:

0.602

Gnomad AMR exome

AF:

0.158

Gnomad ASJ exome

AF:

0.234

Gnomad EAS exome

AF:

0.0363

Gnomad FIN exome

AF:

0.266

Gnomad NFE exome

AF:

0.209

Gnomad OTH exome

AF:

0.209

GnomAD4 exome

AF:

0.212

AC:

64467

AN:

304386

Hom.:

7839

Cov.:

AF XY:

0.208

AC XY:

35979

AN XY:

173324

show subpopulations

African (AFR)

AF:

0.591

AC:

5095

AN:

8628

American (AMR)

AF:

0.156

AC:

4264

AN:

27282

Ashkenazi Jewish (ASJ)

AF:

0.234

AC:

2528

AN:

10790

East Asian (EAS)

AF:

0.0375

AC:

345

AN:

9208

South Asian (SAS)

AF:

0.187

AC:

11195

AN:

59744

European-Finnish (FIN)

AF:

0.266

AC:

3405

AN:

12790

Middle Eastern (MID)

AF:

0.258

AC:

719

AN:

2782

European-Non Finnish (NFE)

AF:

0.212

AC:

33637

AN:

158922

Other (OTH)

AF:

0.230

AC:

3279

AN:

14240

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

3627

7254

10880

14507

18134

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

232

464

696

928

1160

<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:

0.312

AC:

47525

AN:

152126

Hom.:

9752

Cov.:

AF XY:

0.307

AC XY:

22852

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.588

AC:

24373

AN:

41468

American (AMR)

AF:

0.205

AC:

3135

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.217

AC:

754

AN:

3470

East Asian (EAS)

AF:

0.0373

AC:

193

AN:

5180

South Asian (SAS)

AF:

0.179

AC:

863

AN:

4822

European-Finnish (FIN)

AF:

0.249

AC:

2639

AN:

10590

Middle Eastern (MID)

AF:

0.265

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.216

AC:

14721

AN:

67996

Other (OTH)

AF:

0.294

AC:

620

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1480

2960

4441

5921

7401

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

428

856

1284

1712

2140

<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:

0.236

Hom.:

20831

Bravo

AF:

0.319

Asia WGS

AF:

0.148

AC:

514

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.11

(source)

DANN

Benign

0.58

PhyloP100

-1.0

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