Genetic Variant AGPAT1:c.*506A>C (chr6-32168770-T-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_006411.4(AGPAT1):c.*506A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 155,158 control chromosomes in the GnomAD database, including 31,887 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 0.64 ( 31367 hom., cov: 31)

Exomes 𝑓: 0.55 ( 520 hom. )

Consequence

AGPAT1
NM_006411.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.29

Publications

65 publications found

Variant links:

Genes affected

AGPAT1 (HGNC:324): (1-acylglycerol-3-phosphate O-acyltransferase 1) This gene encodes an enzyme that converts lysophosphatidic acid (LPA) into phosphatidic acid (PA). LPA and PA are two phospholipids involved in signal transduction and in lipid biosynthesis in cells. This enzyme localizes to the endoplasmic reticulum. This gene is located in the class III region of the human major histocompatibility complex. Alternative splicing results in two transcript variants encoding the same protein. [provided by RefSeq, Jul 2008]

AGPAT1 links:

PPT2-EGFL8 (HGNC:48343): (PPT2-EGFL8 readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring PPT2 (palmitoyl-protein thioesterase 2) and EGFL8 (EGF-like-domain, multiple 8) genes located in the major histocompatibility complex class III region of chromosome 6. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus unlikely to produce a protein product. [provided by RefSeq, Feb 2011]

PPT2-EGFL8 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=-0.82).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGPAT1	NM_006411.4 link	c.*506A>C		3_prime_UTR_variant	Exon 7 of 7	ENST00000375107.8	NP_006402.1	Q99943A0A024RCV5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AGPAT1	ENST00000375107.8 link	c.*506A>C		3_prime_UTR_variant	Exon 7 of 7	1	NM_006411.4	ENSP00000364248.3		Q99943
PPT2-EGFL8	ENST00000422437.5 link	n.*1378+234T>G		intron_variant	Intron 17 of 20	5		ENSP00000457534.1

Frequencies

GnomAD3 genomes

AF:

0.641

AC:

97273

AN:

151750

Hom.:

31352

Cov.:

show subpopulations

Gnomad AFR

AF:

0.675

Gnomad AMI

AF:

0.704

Gnomad AMR

AF:

0.631

Gnomad ASJ

AF:

0.747

Gnomad EAS

AF:

0.585

Gnomad SAS

AF:

0.685

Gnomad FIN

AF:

0.574

Gnomad MID

AF:

0.778

Gnomad NFE

AF:

0.626

Gnomad OTH

AF:

0.685

GnomAD4 exome

AF:

0.550

AC:

1808

AN:

3288

Hom.:

520

Cov.:

AF XY:

0.560

AC XY:

959

AN XY:

1712

show subpopulations

African (AFR)

AF:

0.630

AC:

AN:

American (AMR)

AF:

0.505

AC:

331

AN:

656

Ashkenazi Jewish (ASJ)

AF:

0.543

AC:

AN:

East Asian (EAS)

AF:

0.423

AC:

AN:

104

South Asian (SAS)

AF:

0.665

AC:

133

AN:

200

European-Finnish (FIN)

AF:

0.536

AC:

AN:

110

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.559

AC:

1101

AN:

1970

Other (OTH)

AF:

0.552

AC:

AN:

154

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

104

138

173

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.641

AC:

97347

AN:

151870

Hom.:

31367

Cov.:

AF XY:

0.640

AC XY:

47489

AN XY:

74226

show subpopulations

African (AFR)

AF:

0.675

AC:

27969

AN:

41438

American (AMR)

AF:

0.631

AC:

9638

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.747

AC:

2589

AN:

3468

East Asian (EAS)

AF:

0.585

AC:

3010

AN:

5142

South Asian (SAS)

AF:

0.684

AC:

3292

AN:

4816

European-Finnish (FIN)

AF:

0.574

AC:

6060

AN:

10554

Middle Eastern (MID)

AF:

0.762

AC:

224

AN:

294

European-Non Finnish (NFE)

AF:

0.626

AC:

42474

AN:

67856

Other (OTH)

AF:

0.687

AC:

1449

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

1739

3478

5217

6956

8695

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.637

Hom.:

120704

Bravo

AF:

0.649

Asia WGS

AF:

0.666

AC:

2320

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

(source)

DANN

Benign

0.72

PhyloP100

1.3

Mutation Taster

=100/0

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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6-32168770-T-G

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