rs10510638

Variant names:

• chr3-30734774-T-C
• rs10510638
• NM_207359.3:c.1393-6359A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.94).
• 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 rank	MANE	Protein	UniProt
GADL1	NM_207359.3	c.1393-6359A>G		intron_variant	Intron 14 of 14	ENST00000282538.10	NP_997242.2
GADL1	XM_017006297.2	c.1336-6359A>G		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.1393-6359A>G		intron_variant	Intron 14 of 14	5	NM_207359.3	ENSP00000282538.5
GADL1	ENST00000498387.1	n.450-6359A>G		intron_variant	Intron 2 of 2	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

African (AFR) AF: 0.284 AC: 11783 AN: 41462

American (AMR) AF: 0.0387 AC: 592 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0438 AC: 152 AN: 3468

East Asian (EAS) AF: 0.0141 AC: 73 AN: 5178

South Asian (SAS) AF: 0.0423 AC: 204 AN: 4828

European-Finnish (FIN) AF: 0.00734 AC: 78 AN: 10624

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0128 AC: 868 AN: 68010

Other (OTH) AF: 0.0705 AC: 149 AN: 2112

Alfa AF: 0.0377 Hom.: 1681

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
PhyloP100		-0.44
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: rs10510638; hg19: chr3-30776266;