rs6482538

chr10-26220935-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.520+1659A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 152,184 control chromosomes in the GnomAD database, including 7,011 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 (7011 hom., cov: 33)
• Consequence: GAD2 NM_001134366.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.750

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAD2	NM_001134366.2	c.520+1659A>G		intron_variant		ENST00000376261.8
GAD2	NM_000818.3	c.520+1659A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAD2	ENST00000376261.8	c.520+1659A>G		intron_variant		1	NM_001134366.2	P1
GAD2	ENST00000259271.7	c.520+1659A>G		intron_variant		1		P1
GAD2	ENST00000648567.1	c.178+1659A>G		intron_variant
GAD2	ENST00000376248.1	n.367+1659A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33096 AN: 152066 Hom.: 6981 Cov.: 33

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0994

Gnomad EAS AF: 0.0507

Gnomad SAS AF: 0.0290

Gnomad FIN AF: 0.0703

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0881

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.218 AC: 33178 AN: 152184 Hom.: 7011 Cov.: 33 AF XY: 0.213 AC XY: 15849 AN XY: 74422

Gnomad4 AFR AF: 0.556

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.0994

Gnomad4 EAS AF: 0.0507

Gnomad4 SAS AF: 0.0286

Gnomad4 FIN AF: 0.0703

Gnomad4 NFE AF: 0.0881

Gnomad4 OTH AF: 0.185

Alfa AF: 0.139 Hom.: 924

Bravo AF: 0.243

Asia WGS AF: 0.0880 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.51
Dann	Benign	0.65

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: rs6482538; hg19: chr10-26509864;