rs1061808

Positions:

• chr6-32168770-T-G

Variant summary

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

The NM_006411.4(AGPAT1):​c.*506A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 155,158 control chromosomes in the GnomAD database, including 31,887 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 0.64 (31367 hom., cov: 31)
  • Exomes 𝑓: 0.55 (520 hom.)
• Consequence: AGPAT1 NM_006411.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29

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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AGPAT1	NM_006411.4	c.*506A>C		3_prime_UTR_variant	7/7	ENST00000375107.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AGPAT1	ENST00000375107.8	c.*506A>C		3_prime_UTR_variant	7/7	1	NM_006411.4	P1

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97273 AN: 151750 Hom.: 31352 Cov.: 31

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.685

GnomAD4 exome AF: 0.550 AC: 1808 AN: 3288 Hom.: 520 Cov.: 0 AF XY: 0.560 AC XY: 959 AN XY: 1712

Gnomad4 AFR exome AF: 0.630

Gnomad4 AMR exome AF: 0.505

Gnomad4 ASJ exome AF: 0.543

Gnomad4 EAS exome AF: 0.423

Gnomad4 SAS exome AF: 0.665

Gnomad4 FIN exome AF: 0.536

Gnomad4 NFE exome AF: 0.559

Gnomad4 OTH exome AF: 0.552

GnomAD4 genome AF: 0.641 AC: 97347 AN: 151870 Hom.: 31367 Cov.: 31 AF XY: 0.640 AC XY: 47489 AN XY: 74226

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.684

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.687

Alfa AF: 0.643 Hom.: 47257

Bravo AF: 0.649

Asia WGS AF: 0.666 AC: 2320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1061808; hg19: chr6-32136547; COSMIC: COSV105213183; COSMIC: COSV105213183;