rs10869127

chr9-72132871-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001242507.3(GDA):c.-100+18038G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,114 control chromosomes in the GnomAD database, including 2,468 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 0.16 (2468 hom., cov: 32)
• Consequence: GDA NM_001242507.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GDA	NM_001242507.3	c.-100+18038G>T		intron_variant
GDA	XM_017015338.2	c.-144+18038G>T		intron_variant
GDA	XM_047424104.1	c.-140+18038G>T		intron_variant
GDA	XM_047424109.1	c.-96+18038G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GDA	ENST00000545168.5	c.-100+18038G>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23875 AN: 151994 Hom.: 2474 Cov.: 32

Gnomad AFR AF: 0.0770

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.157 AC: 23869 AN: 152114 Hom.: 2468 Cov.: 32 AF XY: 0.161 AC XY: 11991 AN XY: 74360

Gnomad4 AFR AF: 0.0769

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.155

Alfa AF: 0.166 Hom.: 2578

Bravo AF: 0.152

Asia WGS AF: 0.374 AC: 1298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.2
Dann	Benign	0.70

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10869127; hg19: chr9-74747787;