4-83544460-C-T

Variant names:

• chr4-83544460-C-T
• rs10516690
• NM_032717.5:c.142-76C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 21 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GPAT3	NM_032717.5	c.142-76C>T		intron_variant	Intron 1 of 11	ENST00000264409.5	NP_116106.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPAT3	ENST00000264409.5	c.142-76C>T		intron_variant	Intron 1 of 11	1	NM_032717.5	ENSP00000264409.4

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

African (AFR) AF: 0.182 AC: 5392 AN: 29572

American (AMR) AF: 0.294 AC: 13059 AN: 44374

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 12757 AN: 24942

East Asian (EAS) AF: 0.303 AC: 11726 AN: 38646

South Asian (SAS) AF: 0.388 AC: 31897 AN: 82244

European-Finnish (FIN) AF: 0.362 AC: 19170 AN: 52944

Middle Eastern (MID) AF: 0.482 AC: 2365 AN: 4910

European-Non Finnish (NFE) AF: 0.406 AC: 384261 AN: 947356

Other (OTH) AF: 0.388 AC: 21123 AN: 54422

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

African (AFR) AF: 0.190 AC: 7897 AN: 41472

American (AMR) AF: 0.349 AC: 5338 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1763 AN: 3468

East Asian (EAS) AF: 0.262 AC: 1355 AN: 5180

South Asian (SAS) AF: 0.360 AC: 1737 AN: 4826

European-Finnish (FIN) AF: 0.374 AC: 3942 AN: 10532

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27324 AN: 67966

Other (OTH) AF: 0.394 AC: 833 AN: 2112

Alfa AF: 0.388 Hom.: 49778

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
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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