chr11-75798591-GGTA-G

Variant names:

• chr11-75798591-GGTA-G
• rs3841596
• NM_032564.5:c.1012+170_1012+172delTAG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_032564.5(DGAT2):​c.1012+170_1012+172delTAG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,170 control chromosomes in the GnomAD database, including 935 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (935 hom., cov: 31)
• Consequence: DGAT2 NM_032564.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112
• Publications: 1 publications found

Genes affected

DGAT2 (HGNC:16940): (diacylglycerol O-acyltransferase 2) This gene encodes one of two enzymes which catalyzes the final reaction in the synthesis of triglycerides in which diacylglycerol is covalently bound to long chain fatty acyl-CoAs. The encoded protein catalyzes this reaction at low concentrations of magnesium chloride while the other enzyme has high activity at high concentrations of magnesium chloride. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

DGAT2 Gene-Disease associations (from GenCC):

• Charcot-Marie-Tooth disease

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

UVRAG-DT (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032564.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGAT2	NM_032564.5	MANE Select	c.1012+170_1012+172delTAG		intron	N/A	NP_115953.2
	DGAT2	NM_001253891.2		c.883+170_883+172delTAG		intron	N/A	NP_001240820.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGAT2	ENST00000228027.12	TSL:1 MANE Select	c.1012+163_1012+165delGTA		intron	N/A	ENSP00000228027.6
	DGAT2	ENST00000376262.7	TSL:1	c.883+163_883+165delGTA		intron	N/A	ENSP00000365438.3
	DGAT2	ENST00000604733.5	TSL:1	c.874+163_874+165delGTA		intron	N/A	ENSP00000474668.1

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16365 AN: 152052 Hom.: 937 Cov.: 31

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.0934

Gnomad FIN AF: 0.0731

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0959

Gnomad OTH AF: 0.0993

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

GnomAD4 genome AF: 0.108 AC: 16372 AN: 152170 Hom.: 935 Cov.: 31 AF XY: 0.106 AC XY: 7860 AN XY: 74382

African (AFR) AF: 0.124 AC: 5145 AN: 41522

American (AMR) AF: 0.102 AC: 1563 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0960 AC: 333 AN: 3470

East Asian (EAS) AF: 0.223 AC: 1151 AN: 5154

South Asian (SAS) AF: 0.0929 AC: 448 AN: 4824

European-Finnish (FIN) AF: 0.0731 AC: 776 AN: 10610

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0959 AC: 6523 AN: 67996

Other (OTH) AF: 0.101 AC: 213 AN: 2116

Alfa AF: 0.111 Hom.: 111

Bravo AF: 0.111

Asia WGS AF: 0.170 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.11
Mutation Taster		=100/0	polymorphism (auto)

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: rs3841596; hg19: chr11-75509636;