rs749540

chr8-41623577-G-Achr8-41623577-G-C

Variant summary

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

The NM_178819.4(GPAT4):c.*2576G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 152,086 control chromosomes in the GnomAD database, including 23,366 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 0.55 (23366 hom., cov: 33)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: GPAT4 NM_178819.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

GPAT4 (HGNC:20880): (glycerol-3-phosphate acyltransferase 4) Lysophosphatidic acid acyltransferases (EC 2.3.1.51) catalyze the conversion of lysophosphatidic acid (LPA) to phosphatidic acid (PA). LPA and PA are involved in signal transduction and lipid biosynthesis.[supplied by OMIM, Apr 2004]

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 (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPAT4	NM_178819.4	c.*2576G>A		3_prime_UTR_variant	13/13	ENST00000396987.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPAT4	ENST00000396987.7	c.*2576G>A		3_prime_UTR_variant	13/13	1	NM_178819.4	P1

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83241 AN: 151962 Hom.: 23332 Cov.: 33

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.580

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.548 AC: 83325 AN: 152080 Hom.: 23366 Cov.: 33 AF XY: 0.540 AC XY: 40106 AN XY: 74330

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.580

Alfa AF: 0.371 Hom.: 871

Bravo AF: 0.564

Asia WGS AF: 0.438 AC: 1521 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	0.33
Dann	Benign	0.58

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: rs749540; hg19: chr8-41481096;