3-30734774-T-C

Position:

• chr3-30734774-T-C

Variant summary

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

The NM_207359.3(GADL1):​c.1393-6359A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0915 in 152,178 control chromosomes in the GnomAD database, including 1,759 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 0.091 (1759 hom., cov: 32)
• Consequence: GADL1 NM_207359.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442

Genes affected

GADL1 (HGNC:27949): (glutamate decarboxylase like 1) Predicted to enable aspartate 1-decarboxylase activity; pyridoxal phosphate binding activity; and sulfinoalanine decarboxylase activity. Predicted to be involved in carboxylic acid metabolic process. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

GADL1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GADL1	NM_207359.3	c.1393-6359A>G		intron_variant		ENST00000282538.10	NP_997242.2
GADL1	XM_017006297.2	c.1336-6359A>G		intron_variant			XP_016861786.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GADL1	ENST00000282538.10	c.1393-6359A>G		intron_variant		5	NM_207359.3	ENSP00000282538.5
GADL1	ENST00000498387.1	n.450-6359A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0915 AC: 13906 AN: 152060 Hom.: 1754 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0388

Gnomad ASJ AF: 0.0438

Gnomad EAS AF: 0.0143

Gnomad SAS AF: 0.0422

Gnomad FIN AF: 0.00734

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0128

Gnomad OTH AF: 0.0713

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

GnomAD4 genome AF: 0.0915 AC: 13924 AN: 152178 Hom.: 1759 Cov.: 32 AF XY: 0.0896 AC XY: 6668 AN XY: 74434

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.0387

Gnomad4 ASJ AF: 0.0438

Gnomad4 EAS AF: 0.0141

Gnomad4 SAS AF: 0.0423

Gnomad4 FIN AF: 0.00734

Gnomad4 NFE AF: 0.0128

Gnomad4 OTH AF: 0.0705

Alfa AF: 0.0233 Hom.: 316

Bravo AF: 0.102

Asia WGS AF: 0.0620 AC: 215 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	2.0
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: rs10510638; hg19: chr3-30776266;