rs56051278

chr2-156525242-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000408.5(GPD2):c.661+11746A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,136 control chromosomes in the GnomAD database, including 4,388 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 0.22 (4388 hom., cov: 32)
• Consequence: GPD2 NM_000408.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267

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 (SAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPD2	NM_000408.5	c.661+11746A>G		intron_variant		ENST00000438166.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPD2	ENST00000438166.7	c.661+11746A>G		intron_variant		1	NM_000408.5	P1

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33966 AN: 152018 Hom.: 4391 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.223 AC: 33953 AN: 152136 Hom.: 4388 Cov.: 32 AF XY: 0.228 AC XY: 16987 AN XY: 74348

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.224

Alfa AF: 0.253 Hom.: 1050

Bravo AF: 0.202

Asia WGS AF: 0.242 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.0
Dann	Benign	0.56

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: rs56051278; hg19: chr2-157381754;