3-30765182-A-G

Variant names:

• chr3-30765182-A-G
• rs304838
• NM_207359.3:c.1392+12997T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GADL1	NM_207359.3	c.1392+12997T>C		intron_variant	Intron 14 of 14	ENST00000282538.10	NP_997242.2
GADL1	XM_017006297.2	c.1335+12997T>C		intron_variant	Intron 14 of 14		XP_016861786.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GADL1	ENST00000282538.10	c.1392+12997T>C		intron_variant	Intron 14 of 14	5	NM_207359.3	ENSP00000282538.5
GADL1	ENST00000498387.1	n.449+12997T>C		intron_variant	Intron 2 of 2	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

African (AFR) AF: 0.419 AC: 17354 AN: 41398

American (AMR) AF: 0.441 AC: 6741 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1716 AN: 3470

East Asian (EAS) AF: 0.353 AC: 1825 AN: 5164

South Asian (SAS) AF: 0.394 AC: 1901 AN: 4820

European-Finnish (FIN) AF: 0.392 AC: 4137 AN: 10554

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.441 AC: 29962 AN: 67946

Other (OTH) AF: 0.464 AC: 980 AN: 2112

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
PhyloP100		-0.41
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs304838; hg19: chr3-30806674;