rs10516690

Positions:

• chr4-83544460-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.142-76C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 1,431,446 control chromosomes in the GnomAD database, including 109,891 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 0.33 (9304 hom., cov: 32)
  • Exomes 𝑓: 0.39 (100587 hom.)
• Consequence: GPAT3 NM_032717.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPAT3	NM_032717.5	c.142-76C>T		intron_variant		ENST00000264409.5	NP_116106.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPAT3	ENST00000264409.5	c.142-76C>T		intron_variant		1	NM_032717.5	ENSP00000264409	P1

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50665 AN: 151918 Hom.: 9306 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.397

GnomAD4 exome AF: 0.392 AC: 501750 AN: 1279410 Hom.: 100587 AF XY: 0.393 AC XY: 254287 AN XY: 646454

Gnomad4 AFR exome AF: 0.182

Gnomad4 AMR exome AF: 0.294

Gnomad4 ASJ exome AF: 0.511

Gnomad4 EAS exome AF: 0.303

Gnomad4 SAS exome AF: 0.388

Gnomad4 FIN exome AF: 0.362

Gnomad4 NFE exome AF: 0.406

Gnomad4 OTH exome AF: 0.388

GnomAD4 genome AF: 0.333 AC: 50666 AN: 152036 Hom.: 9304 Cov.: 32 AF XY: 0.331 AC XY: 24599 AN XY: 74312

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.394

Alfa AF: 0.402 Hom.: 25752

Bravo AF: 0.328

Asia WGS AF: 0.305 AC: 1062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.35
DANN	Benign	0.36

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: rs10516690; hg19: chr4-84465613; COSMIC: COSV52356703;