chr6-32168770-T-G

Variant names:

• chr6-32168770-T-G
• rs1061808
• NM_006411.4:c.*506A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 65 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]

PPT2-EGFL8 (HGNC:48343): (PPT2-EGFL8 readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring PPT2 (palmitoyl-protein thioesterase 2) and EGFL8 (EGF-like-domain, multiple 8) genes located in the major histocompatibility complex class III region of chromosome 6. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus unlikely to produce a protein product. [provided by RefSeq, Feb 2011]

ACMG classification

Our verdict: Benign. The variant received -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.

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.*506A>C		3_prime_UTR	Exon 7 of 7	NP_006402.1
	AGPAT1	NM_001371437.1		c.*506A>C		3_prime_UTR	Exon 7 of 7	NP_001358366.1
	AGPAT1	NM_001371438.1		c.*506A>C		3_prime_UTR	Exon 7 of 7	NP_001358367.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AGPAT1	ENST00000375107.8	TSL:1 MANE Select	c.*506A>C		3_prime_UTR	Exon 7 of 7	ENSP00000364248.3
	AGPAT1	ENST00000336984.6	TSL:1	c.*506A>C		3_prime_UTR	Exon 7 of 7	ENSP00000337463.6
	PPT2-EGFL8	ENST00000422437.5	TSL:5	n.*1378+234T>G		intron	N/A	ENSP00000457534.1

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

African (AFR) AF: 0.630 AC: 29 AN: 46

American (AMR) AF: 0.505 AC: 331 AN: 656

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 25 AN: 46

East Asian (EAS) AF: 0.423 AC: 44 AN: 104

South Asian (SAS) AF: 0.665 AC: 133 AN: 200

European-Finnish (FIN) AF: 0.536 AC: 59 AN: 110

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.559 AC: 1101 AN: 1970

Other (OTH) AF: 0.552 AC: 85 AN: 154

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

African (AFR) AF: 0.675 AC: 27969 AN: 41438

American (AMR) AF: 0.631 AC: 9638 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2589 AN: 3468

East Asian (EAS) AF: 0.585 AC: 3010 AN: 5142

South Asian (SAS) AF: 0.684 AC: 3292 AN: 4816

European-Finnish (FIN) AF: 0.574 AC: 6060 AN: 10554

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42474 AN: 67856

Other (OTH) AF: 0.687 AC: 1449 AN: 2110

Alfa AF: 0.637 Hom.: 120704

Bravo AF: 0.649

Asia WGS AF: 0.666 AC: 2320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.72
PhyloP100		1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1061808; hg19: chr6-32136547; COSMIC: COSV105213183; COSMIC: COSV105213183;