6-161161503-T-C

Position:

• chr6-161161503-T-C

Variant summary

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

The NM_020133.3(AGPAT4):​c.348+4745A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 456,512 control chromosomes in the GnomAD database, including 17,591 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 0.31 (9752 hom., cov: 33)
  • Exomes 𝑓: 0.21 (7839 hom.)
• Consequence: AGPAT4 NM_020133.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

AGPAT4 (HGNC:20885): (1-acylglycerol-3-phosphate O-acyltransferase 4) This gene encodes a member of the 1-acylglycerol-3-phosphate O-acyltransferase family. This integral membrane protein converts lysophosphatidic acid to phosphatidic acid, the second step in de novo phospholipid biosynthesis. [provided by RefSeq, Jul 2008]

AGPAT4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AGPAT4	NM_020133.3	c.348+4745A>G		intron_variant		ENST00000320285.9	NP_064518.1
AGPAT4-IT1	NR_024277.1	n.480A>G		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AGPAT4	ENST00000320285.9	c.348+4745A>G		intron_variant		1	NM_020133.3	ENSP00000314036.4
AGPAT4	ENST00000366911.9	c.179-7193A>G		intron_variant		1		ENSP00000355878.5
AGPAT4	ENST00000436279.1	n.*83+4074A>G		intron_variant		1		ENSP00000413901.1
AGPAT4	ENST00000624499.2	n.4674A>G		non_coding_transcript_exon_variant	4/4	6

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47454 AN: 152008 Hom.: 9720 Cov.: 33

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.0378

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.298

GnomAD3 exomes AF: 0.205 AC: 28036 AN: 136620 Hom.: 3629 AF XY: 0.202 AC XY: 14997 AN XY: 74166

Gnomad AFR exome AF: 0.602

Gnomad AMR exome AF: 0.158

Gnomad ASJ exome AF: 0.234

Gnomad EAS exome AF: 0.0363

Gnomad SAS exome AF: 0.188

Gnomad FIN exome AF: 0.266

Gnomad NFE exome AF: 0.209

Gnomad OTH exome AF: 0.209

GnomAD4 exome AF: 0.212 AC: 64467 AN: 304386 Hom.: 7839 Cov.: 0 AF XY: 0.208 AC XY: 35979 AN XY: 173324

Gnomad4 AFR exome AF: 0.591

Gnomad4 AMR exome AF: 0.156

Gnomad4 ASJ exome AF: 0.234

Gnomad4 EAS exome AF: 0.0375

Gnomad4 SAS exome AF: 0.187

Gnomad4 FIN exome AF: 0.266

Gnomad4 NFE exome AF: 0.212

Gnomad4 OTH exome AF: 0.230

GnomAD4 genome AF: 0.312 AC: 47525 AN: 152126 Hom.: 9752 Cov.: 33 AF XY: 0.307 AC XY: 22852 AN XY: 74374

Gnomad4 AFR AF: 0.588

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.0373

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.294

Alfa AF: 0.223 Hom.: 9049

Bravo AF: 0.319

Asia WGS AF: 0.148 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.11
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: rs6934457; hg19: chr6-161582535; COSMIC: COSV57247372; COSMIC: COSV57247372;