rs10781090

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr9-72224773-C-A
• chr9-72224773-C-G
• chr9-72224773-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001242505.3(GDA):​c.715-904C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 28)
• Consequence: GDA NM_001242505.3 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001242505.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GDA	NM_004293.5	MANE Select	c.715-904C>A		intron	N/A	NP_004284.1
	GDA	NM_001242505.3		c.715-904C>A		intron	N/A	NP_001229434.1
	GDA	NM_001351572.2		c.715-904C>A		intron	N/A	NP_001338501.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GDA	ENST00000358399.8	TSL:1 MANE Select	c.715-904C>A		intron	N/A	ENSP00000351170.4
	GDA	ENST00000238018.8	TSL:1	c.715-904C>A		intron	N/A	ENSP00000238018.4
	GDA	ENST00000475764.5	TSL:1	n.715-904C>A		intron	N/A	ENSP00000436619.1

Frequencies

GnomAD3 genomes Cov.: 28

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

GnomAD4 genome Cov.: 28

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.1
DANN	Benign	0.31
PhyloP100		1.1

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;