6-161197819-C-T

Variant names:

• chr6-161197819-C-T
• rs16892284
• NM_020133.3:c.179-31402G>A

Variant summary

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

The NM_020133.3(AGPAT4):​c.179-31402G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,102 control chromosomes in the GnomAD database, including 2,522 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 0.15 (2522 hom., cov: 32)
• Consequence: AGPAT4 NM_020133.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.450

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]

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 (AFR) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGPAT4	NM_020133.3	c.179-31402G>A		intron_variant	Intron 2 of 8	ENST00000320285.9	NP_064518.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AGPAT4	ENST00000320285.9	c.179-31402G>A		intron_variant	Intron 2 of 8	1	NM_020133.3	ENSP00000314036.4

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22226 AN: 151984 Hom.: 2514 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.0807

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0324

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0793

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.146 AC: 22258 AN: 152102 Hom.: 2522 Cov.: 32 AF XY: 0.145 AC XY: 10781 AN XY: 74350

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.0806

Gnomad4 ASJ AF: 0.0605

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0326

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.0793

Gnomad4 OTH AF: 0.126

Alfa AF: 0.0617 Hom.: 105

Bravo AF: 0.147

Asia WGS AF: 0.0330 AC: 115 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	6.1
DANN	Benign	0.46

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: rs16892284; hg19: chr6-161618851; COSMIC: COSV57252074;