Variant rs3130283 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006411.4(AGPAT1):c.335-168T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.874 in 1,218,050 control chromosomes in the GnomAD database, including 466,631 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 0.90 ( 61794 hom., cov: 30)

Exomes 𝑓: 0.87 ( 404837 hom. )

Consequence

AGPAT1
NM_006411.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.867

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:

AGPAT1 (HGNC:):

AGPAT1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AGPAT1	NM_006411.4 linkuse as main transcript	c.335-168T>G		intron_variant		ENST00000375107.8	NP_006402.1	Q99943A0A024RCV5

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
AGPAT1	ENST00000375107.8 linkuse as main transcript	c.335-168T>G	intron_variant		1	NM_006411.4	ENSP00000364248.3	Q99943
PPT2-EGFL8	ENST00000422437.5 linkuse as main transcript	n.*2039A>C	non_coding_transcript_exon_variant	20/21	5		ENSP00000457534.1
PPT2-EGFL8	ENST00000422437.5 linkuse as main transcript	n.*2039A>C	3_prime_UTR_variant	20/21	5		ENSP00000457534.1

Frequencies

GnomAD3 genomes

AF:

0.900

AC:

136805

AN:

151980

Hom.:

61732

Cov.:

show subpopulations

Gnomad AFR

AF:

0.958

Gnomad AMI

AF:

0.928

Gnomad AMR

AF:

0.921

Gnomad ASJ

AF:

0.915

Gnomad EAS

AF:

0.929

Gnomad SAS

AF:

0.913

Gnomad FIN

AF:

0.884

Gnomad MID

AF:

0.930

Gnomad NFE

AF:

0.858

Gnomad OTH

AF:

0.915

GnomAD4 exome

AF:

0.870

AC:

927714

AN:

1065952

Hom.:

404837

Cov.:

AF XY:

0.872

AC XY:

470879

AN XY:

539968

show subpopulations

Gnomad4 AFR exome

AF:

0.964

Gnomad4 AMR exome

AF:

0.939

Gnomad4 ASJ exome

AF:

0.914

Gnomad4 EAS exome

AF:

0.906

Gnomad4 SAS exome

AF:

0.922

Gnomad4 FIN exome

AF:

0.869

Gnomad4 NFE exome

AF:

0.856

Gnomad4 OTH exome

AF:

0.873

GnomAD4 genome

AF:

0.900

AC:

136927

AN:

152098

Hom.:

61794

Cov.:

AF XY:

0.902

AC XY:

67033

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.958

Gnomad4 AMR

AF:

0.921

Gnomad4 ASJ

AF:

0.915

Gnomad4 EAS

AF:

0.929

Gnomad4 SAS

AF:

0.913

Gnomad4 FIN

AF:

0.884

Gnomad4 NFE

AF:

0.858

Gnomad4 OTH

AF:

0.917

Alfa

AF:

0.873

Hom.:

44763

Bravo

AF:

0.908

Asia WGS

AF:

0.935

AC:

3252

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

7.1

DANN

Benign

0.81

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over