rs11786297

chr8-41619472-A-Gchr8-41619472-A-T

Variant summary

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

The NM_178819.4(GPAT4):c.1262+495A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0781 in 173,204 control chromosomes in the GnomAD database, including 602 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 0.080 (550 hom., cov: 33)
  • Exomes 𝑓: 0.061 (52 hom.)
• Consequence: GPAT4 NM_178819.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPAT4	NM_178819.4	c.1262+495A>G		intron_variant		ENST00000396987.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPAT4	ENST00000396987.7	c.1262+495A>G		intron_variant		1	NM_178819.4	P1
	ENST00000581909.1	n.546+1485T>C		intron_variant, non_coding_transcript_variant		5
GPAT4	ENST00000518628.1	n.561+121A>G		intron_variant, non_coding_transcript_variant		3
GPAT4	ENST00000521349.1	n.361+495A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0805 AC: 12244 AN: 152142 Hom.: 549 Cov.: 33

Gnomad AFR AF: 0.0901

Gnomad AMI AF: 0.0341

Gnomad AMR AF: 0.0909

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0455

Gnomad FIN AF: 0.0402

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0845

Gnomad OTH AF: 0.104

GnomAD4 exome AF: 0.0606 AC: 1269 AN: 20944 Hom.: 52 AF XY: 0.0612 AC XY: 662 AN XY: 10822

Gnomad4 AFR exome AF: 0.100

Gnomad4 AMR exome AF: 0.0640

Gnomad4 ASJ exome AF: 0.0710

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0373

Gnomad4 FIN exome AF: 0.0289

Gnomad4 NFE exome AF: 0.0712

Gnomad4 OTH exome AF: 0.0704

GnomAD4 genome AF: 0.0805 AC: 12250 AN: 152260 Hom.: 550 Cov.: 33 AF XY: 0.0790 AC XY: 5881 AN XY: 74452

Gnomad4 AFR AF: 0.0901

Gnomad4 AMR AF: 0.0907

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0460

Gnomad4 FIN AF: 0.0402

Gnomad4 NFE AF: 0.0846

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0831 Hom.: 542

Bravo AF: 0.0841

Asia WGS AF: 0.0210 AC: 73 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.4
Dann	Benign	0.26

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: rs11786297; hg19: chr8-41476991;