4-83597405-C-T

Variant names:

• chr4-83597405-C-T
• rs3733329
• NM_032717.5:c.911-25C>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.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
• Publications: 11 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=-0.83).
• 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 rank	MANE	Protein	UniProt
GPAT3	NM_032717.5	c.911-25C>T		intron_variant	Intron 8 of 11	ENST00000264409.5	NP_116106.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPAT3	ENST00000264409.5	c.911-25C>T		intron_variant	Intron 8 of 11	1	NM_032717.5	ENSP00000264409.4
GPAT3	ENST00000395226.6	c.911-25C>T		intron_variant	Intron 9 of 12	1		ENSP00000378651.2
GPAT3	ENST00000611707.4	c.911-25C>T		intron_variant	Intron 9 of 12	5		ENSP00000482571.1

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

GnomAD2 exomes AF: 0.274 AC: 46824 AN: 170776 AF XY: 0.285

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 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

African (AFR) AF: 0.0624 AC: 1486 AN: 23822

American (AMR) AF: 0.261 AC: 6006 AN: 22974

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 6200 AN: 19272

East Asian (EAS) AF: 0.240 AC: 7863 AN: 32802

South Asian (SAS) AF: 0.358 AC: 16399 AN: 45850

European-Finnish (FIN) AF: 0.228 AC: 10542 AN: 46288

Middle Eastern (MID) AF: 0.354 AC: 1377 AN: 3888

European-Non Finnish (NFE) AF: 0.285 AC: 252262 AN: 886554

Other (OTH) AF: 0.276 AC: 12778 AN: 46376

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

African (AFR) AF: 0.0688 AC: 2847 AN: 41392

American (AMR) AF: 0.277 AC: 4230 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1105 AN: 3470

East Asian (EAS) AF: 0.301 AC: 1553 AN: 5160

South Asian (SAS) AF: 0.347 AC: 1661 AN: 4792

European-Finnish (FIN) AF: 0.232 AC: 2425 AN: 10474

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19210 AN: 67910

Other (OTH) AF: 0.273 AC: 577 AN: 2110

Alfa AF: 0.272 Hom.: 5669

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
PhyloP100		0.83
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: rs3733329; hg19: chr4-84518558;