rs11553430

chr6-32168994-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_006411.4(AGPAT1):c.*282G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0159 in 507,700 control chromosomes in the GnomAD database, including 104 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 0.015 (30 hom., cov: 32)
  • Exomes 𝑓: 0.016 (74 hom.)
• Consequence: AGPAT1 NM_006411.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44

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=-0.65).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0151 (2289/152074) while in subpopulation NFE AF= 0.0246 (1672/67966). AF 95% confidence interval is 0.0236. There are 30 homozygotes in gnomad4. There are 1077 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 30 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AGPAT1	NM_006411.4	c.*282G>A		3_prime_UTR_variant	7/7	ENST00000375107.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AGPAT1	ENST00000375107.8	c.*282G>A		3_prime_UTR_variant	7/7	1	NM_006411.4	P1

Frequencies

GnomAD3 genomes AF: 0.0151 AC: 2289 AN: 151956 Hom.: 30 Cov.: 32

Gnomad AFR AF: 0.00430

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0129

Gnomad ASJ AF: 0.00374

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000208

Gnomad FIN AF: 0.0188

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0246

Gnomad OTH AF: 0.0139

GnomAD4 exome AF: 0.0163 AC: 5788 AN: 355626 Hom.: 74 Cov.: 0 AF XY: 0.0155 AC XY: 2853 AN XY: 183702

Gnomad4 AFR exome AF: 0.00385

Gnomad4 AMR exome AF: 0.00768

Gnomad4 ASJ exome AF: 0.00480

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000428

Gnomad4 FIN exome AF: 0.0187

Gnomad4 NFE exome AF: 0.0224

Gnomad4 OTH exome AF: 0.0133

GnomAD4 genome AF: 0.0151 AC: 2289 AN: 152074 Hom.: 30 Cov.: 32 AF XY: 0.0145 AC XY: 1077 AN XY: 74348

Gnomad4 AFR AF: 0.00429

Gnomad4 AMR AF: 0.0129

Gnomad4 ASJ AF: 0.00374

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000208

Gnomad4 FIN AF: 0.0188

Gnomad4 NFE AF: 0.0246

Gnomad4 OTH AF: 0.0138

Alfa AF: 0.0233 Hom.: 41

Bravo AF: 0.0137

Asia WGS AF: 0.00115 AC: 4 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	16
Dann	Benign	0.94
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Publications

LitVar

Other links and lift over

dbSNP: rs11553430; hg19: chr6-32136771;