rs10869127

Variant names:

• chr9-72132871-G-T
• rs10869127
• NM_001242507.3:c.-100+18038G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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=-0.9).
• 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 rank	MANE	Protein	UniProt
GDA	NM_001242507.3	c.-100+18038G>T		intron_variant	Intron 1 of 13		NP_001229436.1
GDA	XM_017015338.2	c.-144+18038G>T		intron_variant	Intron 1 of 16		XP_016870827.1
GDA	XM_047424104.1	c.-140+18038G>T		intron_variant	Intron 1 of 16		XP_047280060.1
GDA	XM_047424109.1	c.-96+18038G>T		intron_variant	Intron 1 of 15		XP_047280065.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GDA	ENST00000545168.5	c.-100+18038G>T		intron_variant	Intron 1 of 13	2		ENSP00000437972.1

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

African (AFR) AF: 0.0769 AC: 3195 AN: 41528

American (AMR) AF: 0.151 AC: 2303 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 709 AN: 3470

East Asian (EAS) AF: 0.507 AC: 2619 AN: 5162

South Asian (SAS) AF: 0.324 AC: 1560 AN: 4820

European-Finnish (FIN) AF: 0.167 AC: 1771 AN: 10574

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11048 AN: 67970

Other (OTH) AF: 0.155 AC: 327 AN: 2108

Alfa AF: 0.162 Hom.: 3096

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
PhyloP100		-0.33
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10869127; hg19: chr9-74747787;