rs3130283

chr6-32170768-A-Cchr6-32170768-A-Gchr6-32170768-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.867

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]

ACMG classification

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	UniProt
AGPAT1	NM_006411.4	c.335-168T>G		intron_variant		ENST00000375107.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AGPAT1	ENST00000375107.8	c.335-168T>G		intron_variant		1	NM_006411.4	P1

Frequencies

GnomAD3 genomes AF: 0.900 AC: 136805 AN: 151980 Hom.: 61732 Cov.: 30

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.: 15 AF XY: 0.872 AC XY: 470879 AN XY: 539968

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.: 30 AF XY: 0.902 AC XY: 67033 AN XY: 74340

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

Other links and lift over

dbSNP: rs3130283; hg19: chr6-32138545; COSMIC: COSV61247052; COSMIC: COSV61247052;