NM_004293.5:c.715-904C>T

Variant names:

• chr9-72224773-C-T
• rs10781090
• NM_004293.5:c.715-904C>T

Variant summary

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

The NM_004293.5(GDA):​c.715-904C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 150,052 control chromosomes in the GnomAD database, including 16,344 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 0.47 (16344 hom., cov: 28)
• Consequence: GDA NM_004293.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GDA	NM_004293.5	c.715-904C>T		intron_variant	Intron 7 of 13	ENST00000358399.8	NP_004284.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GDA	ENST00000358399.8	c.715-904C>T		intron_variant	Intron 7 of 13	1	NM_004293.5	ENSP00000351170.4

Frequencies

GnomAD3 genomes AF: 0.467 AC: 69963 AN: 149960 Hom.: 16346 Cov.: 28

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.467 AC: 70004 AN: 150052 Hom.: 16344 Cov.: 28 AF XY: 0.466 AC XY: 34036 AN XY: 73062

African (AFR) AF: 0.438 AC: 17897 AN: 40822

American (AMR) AF: 0.439 AC: 6598 AN: 15044

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1741 AN: 3464

East Asian (EAS) AF: 0.548 AC: 2804 AN: 5114

South Asian (SAS) AF: 0.507 AC: 2426 AN: 4786

European-Finnish (FIN) AF: 0.449 AC: 4393 AN: 9782

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.480 AC: 32497 AN: 67756

Other (OTH) AF: 0.466 AC: 970 AN: 2082

Alfa AF: 0.463 Hom.: 7005

Bravo AF: 0.465

Asia WGS AF: 0.518 AC: 1801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.8
DANN	Benign	0.41
PhyloP100		1.1
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: rs10781090; hg19: chr9-74839689;