chr9-136673534-T-TCGAGCCCGAGCCCCTGCCCTCGAGCC

Variant names:

• chr9-136673534-T-TCGAGCCCGAGCCCCTGCCCTCGAGCC
• NM_006412.4:c.*217_*218insGGCTCGAGGGCAGGGGCTCGGGCTCG

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_006412.4(AGPAT2):​c.*217_*218insGGCTCGAGGGCAGGGGCTCGGGCTCG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000688 in 290,510 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000069 (0 hom.)
• Consequence: AGPAT2 NM_006412.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960

Genes affected

AGPAT2 (HGNC:325): (1-acylglycerol-3-phosphate O-acyltransferase 2) This gene encodes a member of the 1-acylglycerol-3-phosphate O-acyltransferase family. The protein is located within the endoplasmic reticulum membrane and converts lysophosphatidic acid to phosphatidic acid, the second step in de novo phospholipid biosynthesis. Mutations in this gene have been associated with congenital generalized lipodystrophy (CGL), or Berardinelli-Seip syndrome, a disease characterized by a near absence of adipose tissue and severe insulin resistance. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGPAT2	NM_006412.4	c.*217_*218insGGCTCGAGGGCAGGGGCTCGGGCTCG		3_prime_UTR_variant	Exon 6 of 6	ENST00000371696.7	NP_006403.2
AGPAT2	NM_001012727.2	c.*217_*218insGGCTCGAGGGCAGGGGCTCGGGCTCG		3_prime_UTR_variant	Exon 5 of 5		NP_001012745.1
AGPAT2	XM_047422636.1	c.*217_*218insGGCTCGAGGGCAGGGGCTCGGGCTCG		3_prime_UTR_variant	Exon 6 of 6		XP_047278592.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AGPAT2	ENST00000371696	c.*217_*218insGGCTCGAGGGCAGGGGCTCGGGCTCG		3_prime_UTR_variant	Exon 6 of 6	1	NM_006412.4	ENSP00000360761.2
AGPAT2	ENST00000371694	c.*217_*218insGGCTCGAGGGCAGGGGCTCGGGCTCG		3_prime_UTR_variant	Exon 5 of 5	1		ENSP00000360759.3
AGPAT2	ENST00000472820.1	n.*174_*175insGGCTCGAGGGCAGGGGCTCGGGCTCG		downstream_gene_variant		1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000688 AC: 2 AN: 290510 Hom.: 0 Cov.: 5 AF XY: 0.00 AC XY: 0 AN XY: 148526

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000133

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.0000559

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr9-139567986;