9-136673513-C-T

Variant names:

• chr9-136673513-C-T
• rs56310643
• NM_006412.4:c.*239G>A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BS1 BS2

The NM_006412.4(AGPAT2):​c.*239G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00635 in 412,886 control chromosomes in the GnomAD database, including 46 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.012 (36 hom., cov: 34)
  • Exomes 𝑓: 0.0028 (10 hom.)
• Consequence: AGPAT2 NM_006412.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -3.36

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 Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 9-136673513-C-T is Benign according to our data. Variant chr9-136673513-C-T is described in ClinVar as [Benign]. Clinvar id is 365907.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0124 (1880/152090) while in subpopulation AFR AF= 0.0392 (1629/41554). AF 95% confidence interval is 0.0376. There are 36 homozygotes in gnomad4. There are 909 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 36 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGPAT2	NM_006412.4	c.*239G>A		3_prime_UTR_variant	Exon 6 of 6	ENST00000371696.7	NP_006403.2
AGPAT2	NM_001012727.2	c.*239G>A		3_prime_UTR_variant	Exon 5 of 5		NP_001012745.1
AGPAT2	XM_047422636.1	c.*239G>A		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.*239G>A		3_prime_UTR_variant	Exon 6 of 6	1	NM_006412.4	ENSP00000360761.2
AGPAT2	ENST00000371694	c.*239G>A		3_prime_UTR_variant	Exon 5 of 5	1		ENSP00000360759.3
AGPAT2	ENST00000472820.1	n.*196G>A		downstream_gene_variant		1

Frequencies

GnomAD3 genomes AF: 0.0123 AC: 1872 AN: 151972 Hom.: 36 Cov.: 34

Gnomad AFR AF: 0.0391

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00872

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0000943

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000928

Gnomad OTH AF: 0.00864

GnomAD4 exome AF: 0.00285 AC: 743 AN: 260796 Hom.: 10 Cov.: 4 AF XY: 0.00263 AC XY: 352 AN XY: 133764

Gnomad4 AFR exome AF: 0.0446

Gnomad4 AMR exome AF: 0.00559

Gnomad4 ASJ exome AF: 0.00910

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.000140

Gnomad4 NFE exome AF: 0.00105

Gnomad4 OTH exome AF: 0.00660

GnomAD4 genome AF: 0.0124 AC: 1880 AN: 152090 Hom.: 36 Cov.: 34 AF XY: 0.0122 AC XY: 909 AN XY: 74342

Gnomad4 AFR AF: 0.0392

Gnomad4 AMR AF: 0.00871

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0000943

Gnomad4 NFE AF: 0.000928

Gnomad4 OTH AF: 0.00855

Alfa AF: 0.00671 Hom.: 2

Bravo AF: 0.0141

Asia WGS AF: 0.00202 AC: 7 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:1

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Congenital generalized lipodystrophy type 1 Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.26
DANN	Benign	0.57

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

Publications

LitVar

Other links and lift over

dbSNP: rs56310643; hg19: chr9-139567965;