chr3-30831648-G-A

Position:

• chr3-30831648-G-A

Variant summary

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

The NM_207359.3(GADL1):​c.1050+2205C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,736 control chromosomes in the GnomAD database, including 25,831 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 0.54 (25831 hom., cov: 32)
• Consequence: GADL1 NM_207359.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545

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]

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 = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GADL1	NM_207359.3	c.1050+2205C>T		intron_variant		ENST00000282538.10	NP_997242.2
GADL1	XM_017006297.2	c.993+2205C>T		intron_variant			XP_016861786.1
GADL1	XM_047448071.1	c.1050+2205C>T		intron_variant			XP_047304027.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GADL1	ENST00000282538.10	c.1050+2205C>T		intron_variant		5	NM_207359.3	ENSP00000282538	P1
GADL1	ENST00000454381.3	c.1050+2205C>T		intron_variant		1		ENSP00000427059

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81759 AN: 151618 Hom.: 25769 Cov.: 32

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.540 AC: 81880 AN: 151736 Hom.: 25831 Cov.: 32 AF XY: 0.540 AC XY: 40034 AN XY: 74118

Gnomad4 AFR AF: 0.874

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.690

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.485

Alfa AF: 0.478 Hom.: 2464

Bravo AF: 0.567

Asia WGS AF: 0.630 AC: 2188 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.78

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: rs13318432; hg19: chr3-30873140;