NM_006411.4:c.-9-995G>T

Variant names:

• chr6-32172500-C-A
• rs3130348
• NM_006411.4:c.-9-995G>T

Variant summary

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

The NM_006411.4(AGPAT1):​c.-9-995G>T 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 151,976 control chromosomes in the GnomAD database, including 2,633 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 (2633 hom., cov: 32)
• Consequence: AGPAT1 NM_006411.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.427
• Publications: 11 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006411.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AGPAT1	NM_006411.4	MANE Select	c.-9-995G>T		intron	N/A	NP_006402.1
	AGPAT1	NM_001371437.1		c.4-995G>T		intron	N/A	NP_001358366.1
	AGPAT1	NM_001371438.1		c.-9-995G>T		intron	N/A	NP_001358367.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AGPAT1	ENST00000375107.8	TSL:1 MANE Select	c.-9-995G>T		intron	N/A	ENSP00000364248.3
	AGPAT1	ENST00000336984.6	TSL:1	c.-9-995G>T		intron	N/A	ENSP00000337463.6
	AGPAT1	ENST00000375104.6	TSL:2	c.-9-995G>T		intron	N/A	ENSP00000364245.2

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27488 AN: 151858 Hom.: 2636 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: 0.0395

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.181 AC: 27483 AN: 151976 Hom.: 2633 Cov.: 32 AF XY: 0.174 AC XY: 12921 AN XY: 74278

African (AFR) AF: 0.187 AC: 7747 AN: 41434

American (AMR) AF: 0.118 AC: 1797 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3466

East Asian (EAS) AF: 0.0398 AC: 206 AN: 5182

South Asian (SAS) AF: 0.158 AC: 761 AN: 4824

European-Finnish (FIN) AF: 0.141 AC: 1485 AN: 10520

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

European-Non Finnish (NFE) AF: 0.212 AC: 14381 AN: 67956

Other (OTH) AF: 0.165 AC: 349 AN: 2112

Alfa AF: 0.201 Hom.: 2599

Bravo AF: 0.181

Asia WGS AF: 0.0770 AC: 270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.51
PhyloP100		-0.43
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: rs3130348; hg19: chr6-32140277;