Variant rs41310055 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_001242505.3(GDA):c.1399C>T(p.Pro467Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0251 in 1,608,784 control chromosomes in the GnomAD database, including 644 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/16 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.020 ( 51 hom., cov: 32)

Exomes 𝑓: 0.026 ( 593 hom. )

Consequence

GDA
NM_001242505.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.18

Variant links:

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]

GDA links:

GDA (HGNC:):

GDA links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0037838817).

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0199 (3030/152256) while in subpopulation NFE AF= 0.0299 (2031/68014). AF 95% confidence interval is 0.0288. There are 51 homozygotes in gnomad4. There are 1418 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 51 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GDA	NM_004293.5 linkuse as main transcript	c.*2445C>T		3_prime_UTR_variant	14/14	ENST00000358399.8	NP_004284.1	Q9Y2T3-1A0A024R231

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GDA	ENST00000358399.8 linkuse as main transcript	c.*2445C>T		3_prime_UTR_variant	14/14	1	NM_004293.5	ENSP00000351170.4		Q9Y2T3-1

Frequencies

GnomAD3 genomes

AF:

0.0199

AC:

3030

AN:

152138

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00538

Gnomad AMI

AF:

0.0186

Gnomad AMR

AF:

0.0288

Gnomad ASJ

AF:

0.0276

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00352

Gnomad FIN

AF:

0.0135

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0299

Gnomad OTH

AF:

0.0274

GnomAD3 exomes

AF:

0.0203

AC:

4937

AN:

243642

Hom.:

AF XY:

0.0201

AC XY:

2685

AN XY:

133558

show subpopulations

Gnomad AFR exome

AF:

0.00406

Gnomad AMR exome

AF:

0.0216

Gnomad ASJ exome

AF:

0.0246

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00445

Gnomad FIN exome

AF:

0.0172

Gnomad NFE exome

AF:

0.0293

Gnomad OTH exome

AF:

0.0310

GnomAD4 exome

AF:

0.0257

AC:

37366

AN:

1456528

Hom.:

593

Cov.:

AF XY:

0.0252

AC XY:

18281

AN XY:

724818

show subpopulations

Gnomad4 AFR exome

AF:

0.00455

Gnomad4 AMR exome

AF:

0.0226

Gnomad4 ASJ exome

AF:

0.0253

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00565

Gnomad4 FIN exome

AF:

0.0184

Gnomad4 NFE exome

AF:

0.0295

Gnomad4 OTH exome

AF:

0.0219

GnomAD4 genome

AF:

0.0199

AC:

3030

AN:

152256

Hom.:

Cov.:

AF XY:

0.0190

AC XY:

1418

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.00537

Gnomad4 AMR

AF:

0.0287

Gnomad4 ASJ

AF:

0.0276

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00352

Gnomad4 FIN

AF:

0.0135

Gnomad4 NFE

AF:

0.0299

Gnomad4 OTH

AF:

0.0275

Alfa

AF:

0.0282

Hom.:

102

Bravo

AF:

0.0206

TwinsUK

AF:

0.0291

AC:

108

ALSPAC

AF:

0.0314

AC:

121

ESP6500AA

AF:

0.00285

AC:

ESP6500EA

AF:

0.0286

AC:

114

ExAC

AF:

0.0197

AC:

2280

Asia WGS

AF:

0.00346

AC:

AN:

3478

EpiCase

AF:

0.0318

EpiControl

AF:

0.0334

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.71

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.38

DANN

Benign

0.59

DEOGEN2

Benign

0.0049

.;T;T

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.0068

LIST_S2

Benign

0.49

T;T;T

MetaRNN

Benign

0.0038

T;T;T

MetaSVM

Benign

-1.0

PrimateAI

Benign

0.24

PROVEAN

Benign

-0.17

N;N;N

REVEL

Benign

0.040

Sift

Pathogenic

0.0

D;D;D

Sift4G

Pathogenic

0.0

D;.;D

Polyphen

0.0

B;B;.

Vest4

0.16

MPC

0.36

ClinPred

0.0039

GERP RS

-4.2

gMVP

0.32

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over