rs3733329

chr4-83597405-C-T

Variant summary

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

The NM_032717.5(GPAT3):c.911-25C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 1,279,602 control chromosomes in the GnomAD database, including 50,321 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 0.22 (4687 hom., cov: 31)
  • Exomes 𝑓: 0.28 (45634 hom.)
• Consequence: GPAT3 NM_032717.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.828

Genes affected

GPAT3 (HGNC:28157): (glycerol-3-phosphate acyltransferase 3) This gene encodes a member of the lysophosphatidic acid acyltransferase protein family. The encoded protein is an enzyme which catalyzes the conversion of glycerol-3-phosphate to lysophosphatidic acid in the synthesis of triacylglycerol. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jan 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPAT3	NM_032717.5	c.911-25C>T		intron_variant		ENST00000264409.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPAT3	ENST00000264409.5	c.911-25C>T		intron_variant		1	NM_032717.5	P1
GPAT3	ENST00000395226.6	c.911-25C>T		intron_variant		1		P1
GPAT3	ENST00000611707.4	c.911-25C>T		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34053 AN: 151658 Hom.: 4691 Cov.: 31

Gnomad AFR AF: 0.0690

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.277

GnomAD3 exomes AF: 0.274 AC: 46824 AN: 170776 Hom.: 6890 AF XY: 0.285 AC XY: 27015 AN XY: 94826

Gnomad AFR exome AF: 0.0676

Gnomad AMR exome AF: 0.265

Gnomad ASJ exome AF: 0.317

Gnomad EAS exome AF: 0.314

Gnomad SAS exome AF: 0.361

Gnomad FIN exome AF: 0.231

Gnomad NFE exome AF: 0.284

Gnomad OTH exome AF: 0.284

GnomAD4 exome AF: 0.279 AC: 314913 AN: 1127826 Hom.: 45634 Cov.: 16 AF XY: 0.281 AC XY: 157367 AN XY: 559148

Gnomad4 AFR exome AF: 0.0624

Gnomad4 AMR exome AF: 0.261

Gnomad4 ASJ exome AF: 0.322

Gnomad4 EAS exome AF: 0.240

Gnomad4 SAS exome AF: 0.358

Gnomad4 FIN exome AF: 0.228

Gnomad4 NFE exome AF: 0.285

Gnomad4 OTH exome AF: 0.276

GnomAD4 genome AF: 0.224 AC: 34035 AN: 151776 Hom.: 4687 Cov.: 31 AF XY: 0.227 AC XY: 16848 AN XY: 74138

Gnomad4 AFR AF: 0.0688

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.273

Alfa AF: 0.277 Hom.: 5012

Bravo AF: 0.220

Asia WGS AF: 0.301 AC: 1044 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	6.0
Dann	Benign	0.50

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: rs3733329; hg19: chr4-84518558;