rs16858988

Positions:

• chr2-170846450-G-A

Variant summary

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

The NM_000817.3(GAD1):​c.1002+387G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,178 control chromosomes in the GnomAD database, including 2,938 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 0.18 (2938 hom., cov: 33)
• Consequence: GAD1 NM_000817.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668

Genes affected

GAD1 (HGNC:4092): (glutamate decarboxylase 1) 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 autoantigen and an autoreactive T cell target in insulin-dependent diabetes. This gene may also play a role in the stiff man syndrome. Deficiency in this enzyme has been shown to lead to pyridoxine dependency with seizures. Alternative splicing of this gene results in two products, the predominant 67-kD form and a less-frequent 25-kD form. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GAD1	NM_000817.3	c.1002+387G>A		intron_variant		ENST00000358196.8	NP_000808.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GAD1	ENST00000358196.8	c.1002+387G>A		intron_variant		1	NM_000817.3	ENSP00000350928.3
GAD1	ENST00000493875.5	n.1002+387G>A		intron_variant		1		ENSP00000434696.1
GAD1	ENST00000625689.2	c.1002+387G>A		intron_variant		5		ENSP00000486612.1
GAD1	ENST00000414527.6	n.*187+387G>A		intron_variant		5		ENSP00000403849.1

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27133 AN: 152060 Hom.: 2937 Cov.: 33

Gnomad AFR AF: 0.0714

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.178 AC: 27142 AN: 152178 Hom.: 2938 Cov.: 33 AF XY: 0.184 AC XY: 13677 AN XY: 74374

Gnomad4 AFR AF: 0.0712

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.166

Alfa AF: 0.209 Hom.: 7222

Bravo AF: 0.158

Asia WGS AF: 0.272 AC: 944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	4.3
DANN	Benign	0.64

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: rs16858988; hg19: chr2-171702960;