chr8-41589951-T-G

Variant names:

• chr8-41589951-T-G
• rs7837006
• NM_178819.4:c.-848-8341T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GPAT4	NM_178819.4	c.-848-8341T>G		intron_variant	Intron 1 of 12	ENST00000396987.7	NP_848934.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPAT4	ENST00000396987.7	c.-848-8341T>G		intron_variant	Intron 1 of 12	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

African (AFR) AF: 0.552 AC: 22852 AN: 41420

American (AMR) AF: 0.426 AC: 6512 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1788 AN: 3468

East Asian (EAS) AF: 0.469 AC: 2417 AN: 5150

South Asian (SAS) AF: 0.386 AC: 1861 AN: 4818

European-Finnish (FIN) AF: 0.342 AC: 3618 AN: 10582

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30298 AN: 67962

Other (OTH) AF: 0.475 AC: 1001 AN: 2108

Alfa AF: 0.458 Hom.: 67588

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
PhyloP100		-0.071
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: rs7837006; hg19: chr8-41447470;