Variant 9-136687306-CCAGCAGCAG-CCAGCAGCAGCAG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_006412.4(AGPAT2):c.49_51dupCTG(p.Leu17dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0877 in 1,575,438 control chromosomes in the GnomAD database, including 5,825 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.069 ( 464 hom., cov: 32)

Exomes 𝑓: 0.090 ( 5361 hom. )

Consequence

AGPAT2
NM_006412.4 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -2.28

Variant links:

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]

AGPAT2 links:

AGPAT2 (HGNC:):

AGPAT2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 9-136687306-C-CCAG is Benign according to our data. Variant chr9-136687306-C-CCAG is described in ClinVar as [Likely_benign]. Clinvar id is 259977.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AGPAT2	NM_006412.4 linkuse as main transcript	c.49_51dupCTG	p.Leu17dup	conservative_inframe_insertion	1/6	ENST00000371696.7	NP_006403.2	O15120-1A0A024R8I7
AGPAT2	NM_001012727.2 linkuse as main transcript	c.49_51dupCTG	p.Leu17dup	conservative_inframe_insertion	1/5		NP_001012745.1	O15120-2A0A024R8F9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
AGPAT2	ENST00000371696.7 linkuse as main transcript	c.49_51dupCTG	p.Leu17dup	conservative_inframe_insertion	1/6	1	NM_006412.4	ENSP00000360761.2	O15120-1
AGPAT2	ENST00000371694.7 linkuse as main transcript	c.49_51dupCTG	p.Leu17dup	conservative_inframe_insertion	1/5	1		ENSP00000360759.3	O15120-2
AGPAT2	ENST00000470861.1 linkuse as main transcript	n.57_59dupCTG		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes

AF:

0.0695

AC:

10544

AN:

151760

Hom.:

461

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0264

Gnomad AMI

AF:

0.0471

Gnomad AMR

AF:

0.0807

Gnomad ASJ

AF:

0.103

Gnomad EAS

AF:

0.0386

Gnomad SAS

AF:

0.0438

Gnomad FIN

AF:

0.0467

Gnomad MID

AF:

0.0924

Gnomad NFE

AF:

0.0984

Gnomad OTH

AF:

0.100

GnomAD3 exomes

AF:

0.0731

AC:

13771

AN:

188298

Hom.:

388

AF XY:

0.0739

AC XY:

7845

AN XY:

106162

show subpopulations

Gnomad AFR exome

AF:

0.0236

Gnomad AMR exome

AF:

0.0789

Gnomad ASJ exome

AF:

0.0900

Gnomad EAS exome

AF:

0.0346

Gnomad SAS exome

AF:

0.0457

Gnomad FIN exome

AF:

0.0428

Gnomad NFE exome

AF:

0.0936

Gnomad OTH exome

AF:

0.0861

GnomAD4 exome

AF:

0.0897

AC:

127686

AN:

1423566

Hom.:

5361

Cov.:

AF XY:

0.0887

AC XY:

62796

AN XY:

707946

show subpopulations

Gnomad4 AFR exome

AF:

0.0247

Gnomad4 AMR exome

AF:

0.0772

Gnomad4 ASJ exome

AF:

0.0930

Gnomad4 EAS exome

AF:

0.0315

Gnomad4 SAS exome

AF:

0.0469

Gnomad4 FIN exome

AF:

0.0482

Gnomad4 NFE exome

AF:

0.0987

Gnomad4 OTH exome

AF:

0.0886

GnomAD4 genome

AF:

0.0695

AC:

10548

AN:

151872

Hom.:

464

Cov.:

AF XY:

0.0660

AC XY:

4901

AN XY:

74220

show subpopulations

Gnomad4 AFR

AF:

0.0266

Gnomad4 AMR

AF:

0.0807

Gnomad4 ASJ

AF:

0.103

Gnomad4 EAS

AF:

0.0383

Gnomad4 SAS

AF:

0.0437

Gnomad4 FIN

AF:

0.0467

Gnomad4 NFE

AF:

0.0984

Gnomad4 OTH

AF:

0.0982

Asia WGS

AF:

0.0490

AC:

169

AN:

3464

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 26, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Congenital generalized lipodystrophy

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over