6-161197819-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.322 AC: 13332 AN: 41440

American (AMR) AF: 0.0806 AC: 1233 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0605 AC: 210 AN: 3470

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5178

South Asian (SAS) AF: 0.0326 AC: 157 AN: 4818

European-Finnish (FIN) AF: 0.151 AC: 1599 AN: 10570

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0793 AC: 5391 AN: 68018

Other (OTH) AF: 0.126 AC: 267 AN: 2112

Alfa AF: 0.0681 Hom.: 144

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
PhyloP100		0.45
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: rs16892284; hg19: chr6-161618851; COSMIC: COSV57252074;