rs3769371

Positions:

• chr2-156556586-C-A
• chr2-156556586-C-G
• chr2-156556586-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPD2	NM_000408.5	c.972-803C>A		intron_variant		ENST00000438166.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPD2	ENST00000438166.7	c.972-803C>A		intron_variant		1	NM_000408.5	P1

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

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.809

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.651

Gnomad4 NFE AF: 0.725

Gnomad4 OTH AF: 0.725

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.70
DANN	Benign	0.32

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: rs3769371; hg19: chr2-157413098;