9-72193094-A-G

Variant names:

• chr9-72193094-A-G
• rs7867133
• NM_004293.5:c.124-2406A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004293.5(GDA):​c.124-2406A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 151,944 control chromosomes in the GnomAD database, including 9,839 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 0.35 (9839 hom., cov: 31)
• Consequence: GDA NM_004293.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 1 publications found

Genes affected

GDA (HGNC:4212): (guanine deaminase) This gene encodes an enzyme responsible for the hydrolytic deamination of guanine. Studies in rat ortholog suggest this gene plays a role in microtubule assembly. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GDA	NM_004293.5	c.124-2406A>G		intron_variant	Intron 1 of 13	ENST00000358399.8	NP_004284.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GDA	ENST00000358399.8	c.124-2406A>G		intron_variant	Intron 1 of 13	1	NM_004293.5	ENSP00000351170.4

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52542 AN: 151824 Hom.: 9835 Cov.: 31

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.346 AC: 52583 AN: 151944 Hom.: 9839 Cov.: 31 AF XY: 0.347 AC XY: 25768 AN XY: 74258

African (AFR) AF: 0.479 AC: 19819 AN: 41410

American (AMR) AF: 0.288 AC: 4406 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1122 AN: 3470

East Asian (EAS) AF: 0.556 AC: 2870 AN: 5160

South Asian (SAS) AF: 0.339 AC: 1631 AN: 4814

European-Finnish (FIN) AF: 0.304 AC: 3207 AN: 10542

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18571 AN: 67954

Other (OTH) AF: 0.306 AC: 646 AN: 2112

Alfa AF: 0.216 Hom.: 632

Bravo AF: 0.350

Asia WGS AF: 0.457 AC: 1588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.12
DANN	Benign	0.66
PhyloP100		-2.0
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: rs7867133; hg19: chr9-74808010; COSMIC: COSV52993241; COSMIC: COSV52993241;