rs3130284

Variant names:

• chr6-32172710-T-C
• rs3130284
• NM_006411.4:c.-9-1205A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006411.4(AGPAT1):​c.-9-1205A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,116 control chromosomes in the GnomAD database, including 2,630 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 0.18 (2630 hom., cov: 32)
• Consequence: AGPAT1 NM_006411.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.45
• Publications: 42 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGPAT1	NM_006411.4	c.-9-1205A>G		intron_variant	Intron 1 of 6	ENST00000375107.8	NP_006402.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AGPAT1	ENST00000375107.8	c.-9-1205A>G		intron_variant	Intron 1 of 6	1	NM_006411.4	ENSP00000364248.3

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27495 AN: 151998 Hom.: 2633 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0394

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.168

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.181 AC: 27490 AN: 152116 Hom.: 2630 Cov.: 32 AF XY: 0.174 AC XY: 12918 AN XY: 74360

African (AFR) AF: 0.187 AC: 7761 AN: 41484

American (AMR) AF: 0.118 AC: 1800 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3472

East Asian (EAS) AF: 0.0397 AC: 206 AN: 5188

South Asian (SAS) AF: 0.157 AC: 758 AN: 4818

European-Finnish (FIN) AF: 0.140 AC: 1482 AN: 10576

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14376 AN: 67972

Other (OTH) AF: 0.166 AC: 350 AN: 2114

Alfa AF: 0.202 Hom.: 12025

Bravo AF: 0.181

Asia WGS AF: 0.0780 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.19
DANN	Benign	0.25
PhyloP100		-3.4
PromoterAI		-0.0086	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3130284; hg19: chr6-32140487;