dbSNP rs3734462: AGPAT4:p.Ser349Ser (chr6-161136630-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_020133.3(AGPAT4):c.1047C>T(p.Ser349Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 1,612,954 control chromosomes in the GnomAD database, including 30,593 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 ( 2298 hom., cov: 33)

Exomes 𝑓: 0.19 ( 28295 hom. )

Consequence

AGPAT4
NM_020133.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0530

Publications

15 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.48).

BP7

Synonymous conserved (PhyloP=-0.053 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGPAT4	NM_020133.3 link	c.1047C>T	p.Ser349Ser	synonymous_variant	Exon 9 of 9	ENST00000320285.9	NP_064518.1	Q9NRZ5-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AGPAT4	ENST00000320285.9 link	c.1047C>T	p.Ser349Ser	synonymous_variant	Exon 9 of 9	1	NM_020133.3	ENSP00000314036.4		Q9NRZ5-1
AGPAT4	ENST00000366911.9 link	c.*520C>T		3_prime_UTR_variant	Exon 8 of 8	1		ENSP00000355878.5		Q6AI25

Frequencies

GnomAD3 genomes

AF:

0.151

AC:

22967

AN:

152122

Hom.:

2293

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0441

Gnomad AMI

AF:

0.111

Gnomad AMR

AF:

0.292

Gnomad ASJ

AF:

0.108

Gnomad EAS

AF:

0.198

Gnomad SAS

AF:

0.0622

Gnomad FIN

AF:

0.157

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.190

Gnomad OTH

AF:

0.144

GnomAD2 exomes

AF:

0.191

AC:

47546

AN:

248986

AF XY:

0.178

show subpopulations

Gnomad AFR exome

AF:

0.0434

Gnomad AMR exome

AF:

0.414

Gnomad ASJ exome

AF:

0.112

Gnomad EAS exome

AF:

0.218

Gnomad FIN exome

AF:

0.158

Gnomad NFE exome

AF:

0.189

Gnomad OTH exome

AF:

0.183

GnomAD4 exome

AF:

0.186

AC:

271511

AN:

1460714

Hom.:

28295

Cov.:

AF XY:

0.181

AC XY:

131396

AN XY:

726716

show subpopulations

African (AFR)

AF:

0.0365

AC:

1221

AN:

33474

American (AMR)

AF:

0.402

AC:

17977

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.107

AC:

2799

AN:

26132

East Asian (EAS)

AF:

0.191

AC:

7574

AN:

39692

South Asian (SAS)

AF:

0.0607

AC:

5239

AN:

86246

European-Finnish (FIN)

AF:

0.157

AC:

8387

AN:

53346

Middle Eastern (MID)

AF:

0.0541

AC:

312

AN:

5766

European-Non Finnish (NFE)

AF:

0.196

AC:

218244

AN:

1110974

Other (OTH)

AF:

0.162

AC:

9758

AN:

60364

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

10440

20879

31319

41758

52198

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7636

15272

22908

30544

38180

<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:

0.151

AC:

22986

AN:

152240

Hom.:

2298

Cov.:

AF XY:

0.150

AC XY:

11146

AN XY:

74434

show subpopulations

African (AFR)

AF:

0.0440

AC:

1830

AN:

41558

American (AMR)

AF:

0.293

AC:

4477

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.108

AC:

373

AN:

3468

East Asian (EAS)

AF:

0.199

AC:

1023

AN:

5152

South Asian (SAS)

AF:

0.0627

AC:

303

AN:

4832

European-Finnish (FIN)

AF:

0.157

AC:

1667

AN:

10596

Middle Eastern (MID)

AF:

0.0544

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.190

AC:

12896

AN:

68012

Other (OTH)

AF:

0.142

AC:

300

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

993

1987

2980

3974

4967

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

254

508

762

1016

1270

<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:

0.177

Hom.:

5315

Bravo

AF:

0.163

Asia WGS

AF:

0.0930

AC:

324

AN:

3478

EpiCase

AF:

0.175

EpiControl

AF:

0.177

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

8.9

(source)

DANN

Benign

0.76

PhyloP100

-0.053

Mutation Taster

=91/9

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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