8-41589951-T-G

Position:

• chr8-41589951-T-G

Variant summary

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

The NM_178819.4(GPAT4):​c.-848-8341T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 152,008 control chromosomes in the GnomAD database, including 16,914 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 0.47 (16914 hom., cov: 32)
• Consequence: GPAT4 NM_178819.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

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]

GPAT4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPAT4	NM_178819.4	c.-848-8341T>G		intron_variant		ENST00000396987.7	NP_848934.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPAT4	ENST00000396987.7	c.-848-8341T>G		intron_variant		1	NM_178819.4	ENSP00000380184.3

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70861 AN: 151890 Hom.: 16889 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.475

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.467 AC: 70929 AN: 152008 Hom.: 16914 Cov.: 32 AF XY: 0.460 AC XY: 34150 AN XY: 74292

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.475

Alfa AF: 0.458 Hom.: 32295

Bravo AF: 0.479

Asia WGS AF: 0.412 AC: 1432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.5
DANN	Benign	0.60

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: rs7837006; hg19: chr8-41447470;