rs7073119

chr10-26268681-A-G

Variant summary

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

The NM_001134366.2(GAD2):c.921-438A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 151,996 control chromosomes in the GnomAD database, including 14,883 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 0.40 (14883 hom., cov: 32)
• Consequence: GAD2 NM_001134366.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151

Genes affected

GAD2 (HGNC:4093): (glutamate decarboxylase 2) This gene encodes one of several forms of glutamic acid decarboxylase, identified as a major autoantigen in insulin-dependent diabetes. The enzyme encoded is responsible for catalyzing the production of gamma-aminobutyric acid from L-glutamic acid. A pathogenic role for this enzyme has been identified in the human pancreas since it has been identified as an autoantibody and an autoreactive T cell target in insulin-dependent diabetes. This gene may also play a role in the stiff man syndrome. Alternative splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Oct 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAD2	NM_001134366.2	c.921-438A>G		intron_variant		ENST00000376261.8
GAD2	NM_000818.3	c.921-438A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAD2	ENST00000376261.8	c.921-438A>G		intron_variant		1	NM_001134366.2	P1
GAD2	ENST00000259271.7	c.921-438A>G		intron_variant		1		P1
GAD2	ENST00000648567.1	c.579-438A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60698 AN: 151878 Hom.: 14852 Cov.: 32

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.400 AC: 60769 AN: 151996 Hom.: 14883 Cov.: 32 AF XY: 0.395 AC XY: 29378 AN XY: 74298

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.386

Alfa AF: 0.346 Hom.: 1740

Bravo AF: 0.423

Asia WGS AF: 0.341 AC: 1188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	6.7
Dann	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7073119; hg19: chr10-26557610;