rs10499316

Variant names:

• chr6-161195591-T-C
• rs10499316
• NM_020133.3:c.179-29174A>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.179-29174A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,118 control chromosomes in the GnomAD database, including 4,368 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 0.18 (4368 hom., cov: 32)
• Consequence: AGPAT4 NM_020133.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGPAT4	NM_020133.3	c.179-29174A>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.179-29174A>G		intron_variant	Intron 2 of 8	1	NM_020133.3	ENSP00000314036.4

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27191 AN: 152000 Hom.: 4349 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.0905

Gnomad ASJ AF: 0.0611

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0332

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0796

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.179 AC: 27256 AN: 152118 Hom.: 4368 Cov.: 32 AF XY: 0.178 AC XY: 13237 AN XY: 74384

African (AFR) AF: 0.437 AC: 18104 AN: 41472

American (AMR) AF: 0.0903 AC: 1381 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0611 AC: 212 AN: 3468

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5180

South Asian (SAS) AF: 0.0332 AC: 160 AN: 4822

European-Finnish (FIN) AF: 0.151 AC: 1600 AN: 10576

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0796 AC: 5410 AN: 68002

Other (OTH) AF: 0.151 AC: 318 AN: 2108

Alfa AF: 0.153 Hom.: 543

Bravo AF: 0.184

Asia WGS AF: 0.0440 AC: 152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.2
DANN	Benign	0.26
PhyloP100		-0.10
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs10499316; hg19: chr6-161616623;