chr2-156556586-C-A

Variant names:

• chr2-156556586-C-A
• rs3769371
• NM_000408.5:c.972-803C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000408.5(GPD2):​c.972-803C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 151,976 control chromosomes in the GnomAD database, including 39,059 homozygotes. 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: 𝑓 0.72 (39059 hom., cov: 32)
• Consequence: GPD2 NM_000408.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153
• Publications: 4 publications found

Genes affected

GPD2 (HGNC:4456): (glycerol-3-phosphate dehydrogenase 2) The protein encoded by this gene localizes to the inner mitochondrial membrane and catalyzes the conversion of glycerol-3-phosphate to dihydroxyacetone phosphate, using FAD as a cofactor. Along with GDP1, the encoded protein constitutes the glycerol phosphate shuttle, which reoxidizes NADH formed during glycolysis. Two transcript variants encoding the same protein have been found for this gene.[provided by RefSeq, Jan 2010]

GPD2 Gene-Disease associations (from GenCC):

• diabetes mellitus, noninsulin-dependent

  Inheritance: AD Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000408.5. 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
	GPD2	NM_000408.5	MANE Select	c.972-803C>A		intron	N/A	NP_000399.3
	GPD2	NM_001083112.3		c.972-803C>A		intron	N/A	NP_001076581.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPD2	ENST00000438166.7	TSL:1 MANE Select	c.972-803C>A		intron	N/A	ENSP00000409708.2
	GPD2	ENST00000310454.10	TSL:1	c.972-803C>A		intron	N/A	ENSP00000308610.5
	GPD2	ENST00000540309.5	TSL:1	c.972-803C>A		intron	N/A	ENSP00000440892.1

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108740 AN: 151856 Hom.: 39013 Cov.: 32

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.716 AC: 108852 AN: 151976 Hom.: 39059 Cov.: 32 AF XY: 0.714 AC XY: 52998 AN XY: 74258

African (AFR) AF: 0.701 AC: 29075 AN: 41450

American (AMR) AF: 0.730 AC: 11149 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2609 AN: 3468

East Asian (EAS) AF: 0.809 AC: 4188 AN: 5174

South Asian (SAS) AF: 0.677 AC: 3259 AN: 4816

European-Finnish (FIN) AF: 0.651 AC: 6861 AN: 10532

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49267 AN: 67950

Other (OTH) AF: 0.725 AC: 1535 AN: 2116

Alfa AF: 0.617 Hom.: 1748

Bravo AF: 0.726

Asia WGS AF: 0.731 AC: 2538 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.70
DANN	Benign	0.32
PhyloP100		-0.15
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: rs3769371; hg19: chr2-157413098;