3-30765182-A-G

Position:

• chr3-30765182-A-G

Variant summary

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

The NM_207359.3(GADL1):​c.1392+12997T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 151,940 control chromosomes in the GnomAD database, including 13,968 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 0.43 (13968 hom., cov: 31)
• Consequence: GADL1 NM_207359.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.405

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GADL1	NM_207359.3	c.1392+12997T>C		intron_variant		ENST00000282538.10	NP_997242.2
GADL1	XM_017006297.2	c.1335+12997T>C		intron_variant			XP_016861786.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GADL1	ENST00000282538.10	c.1392+12997T>C		intron_variant		5	NM_207359.3	ENSP00000282538.5
GADL1	ENST00000498387.1	n.449+12997T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65136 AN: 151822 Hom.: 13958 Cov.: 31

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.429 AC: 65169 AN: 151940 Hom.: 13968 Cov.: 31 AF XY: 0.428 AC XY: 31749 AN XY: 74244

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.464

Alfa AF: 0.326 Hom.: 1116

Bravo AF: 0.433

Asia WGS AF: 0.360 AC: 1257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.78
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: rs304838; hg19: chr3-30806674;