NM_018361.5:c.290-2353G>A

Variant names:

• chr8-6728358-G-A
• rs2980683
• NM_018361.5:c.290-2353G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_018361.5(AGPAT5):​c.290-2353G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)
• Consequence: AGPAT5 NM_018361.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588
• Publications: 5 publications found

Genes affected

AGPAT5 (HGNC:20886): (1-acylglycerol-3-phosphate O-acyltransferase 5) 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. A pseudogene of this gene is present on the Y chromosome. [provided by RefSeq, Aug 2014]

AGPAT5 Gene-Disease associations (from GenCC):

• Tourette syndrome

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGPAT5	NM_018361.5	c.290-2353G>A		intron_variant	Intron 2 of 7	ENST00000285518.11	NP_060831.2
AGPAT5	XM_047421938.1	c.-164-2353G>A		intron_variant	Intron 1 of 6		XP_047277894.1
AGPAT5	XM_047421939.1	c.-164-2353G>A		intron_variant	Intron 3 of 8		XP_047277895.1
AGPAT5	XM_047421940.1	c.290-2353G>A		intron_variant	Intron 2 of 4		XP_047277896.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AGPAT5	ENST00000285518.11	c.290-2353G>A		intron_variant	Intron 2 of 7	1	NM_018361.5	ENSP00000285518.6
AGPAT5	ENST00000518327.1	c.193+19471G>A		intron_variant	Intron 1 of 2	1		ENSP00000430751.1
AGPAT5	ENST00000523234.5	n.220-2353G>A		intron_variant	Intron 1 of 6	5		ENSP00000430016.1
AGPAT5	ENST00000523586.1	n.*222-2353G>A		intron_variant	Intron 3 of 3	4		ENSP00000428152.1

Frequencies

GnomAD3 genomes Cov.: 34

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

GnomAD4 genome Cov.: 34

Alfa AF: 0.00 Hom.: 1606

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.91
PhyloP100		-0.59

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: rs2980683; hg19: chr8-6585879;