6-161187984-T-C

Variant names:

• chr6-161187984-T-C
• rs2064721
• NM_020133.3:c.179-21567A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020133.3(AGPAT4):​c.179-21567A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,178 control chromosomes in the GnomAD database, including 6,418 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 0.27 (6418 hom., cov: 33)
• Consequence: AGPAT4 NM_020133.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 4 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGPAT4	NM_020133.3	c.179-21567A>G		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.179-21567A>G		intron_variant	Intron 2 of 8	1	NM_020133.3	ENSP00000314036.4

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40885 AN: 152060 Hom.: 6416 Cov.: 33

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.269 AC: 40894 AN: 152178 Hom.: 6418 Cov.: 33 AF XY: 0.269 AC XY: 20043 AN XY: 74386

African (AFR) AF: 0.118 AC: 4898 AN: 41548

American (AMR) AF: 0.277 AC: 4228 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1394 AN: 3470

East Asian (EAS) AF: 0.192 AC: 994 AN: 5188

South Asian (SAS) AF: 0.376 AC: 1814 AN: 4828

European-Finnish (FIN) AF: 0.320 AC: 3382 AN: 10566

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22934 AN: 67978

Other (OTH) AF: 0.317 AC: 668 AN: 2110

Alfa AF: 0.312 Hom.: 22233

Bravo AF: 0.256

Asia WGS AF: 0.301 AC: 1045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.029
DANN	Benign	0.49
PhyloP100		-1.4
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: rs2064721; hg19: chr6-161609016;