rs582397

Variant names:

• chr2-156407537-T-C
• rs582397
• ENST00000847773.1:n.525+6968T>C

Variant summary

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

The ENST00000847773.1(ENSG00000310173):​n.525+6968T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,074 control chromosomes in the GnomAD database, including 3,353 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 0.20 (3353 hom., cov: 32)
• Consequence: ENSG00000310173 ENST00000847773.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690
• Publications: 4 publications found

Genes affected

ENSG00000310173 (HGNC:):

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPD2	XM_047443963.1	c.-9+6968T>C		intron_variant	Intron 1 of 16		XP_047299919.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310173	ENST00000847773.1	n.525+6968T>C		intron_variant	Intron 1 of 1
ENSG00000310173	ENST00000847774.1	n.147+6968T>C		intron_variant	Intron 1 of 2
ENSG00000310173	ENST00000847775.1	n.119+6968T>C		intron_variant	Intron 1 of 2
ENSG00000310173	ENST00000847776.1	n.119+6968T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29965 AN: 151956 Hom.: 3346 Cov.: 32

Gnomad AFR AF: 0.0921

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.197 AC: 29976 AN: 152074 Hom.: 3353 Cov.: 32 AF XY: 0.200 AC XY: 14846 AN XY: 74338

African (AFR) AF: 0.0919 AC: 3812 AN: 41496

American (AMR) AF: 0.192 AC: 2941 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1005 AN: 3470

East Asian (EAS) AF: 0.236 AC: 1224 AN: 5176

South Asian (SAS) AF: 0.182 AC: 875 AN: 4816

European-Finnish (FIN) AF: 0.252 AC: 2656 AN: 10550

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16704 AN: 67976

Other (OTH) AF: 0.232 AC: 489 AN: 2108

Alfa AF: 0.221 Hom.: 718

Bravo AF: 0.189

Asia WGS AF: 0.259 AC: 901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.5
DANN	Benign	0.70
PhyloP100		-0.069

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs582397; hg19: chr2-157264049;