dbSNP rs2070388: GART:c.2841+11C>G (chr21-33504401-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000819.5(GART):c.2841+11C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 1,610,698 control chromosomes in the GnomAD database, including 10,573 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 0.092 ( 896 hom., cov: 32)

Exomes 𝑓: 0.11 ( 9677 hom. )

Consequence

GART
NM_000819.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.283

Variant links:

Genes affected

GART (HGNC:4163): (phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase) The protein encoded by this gene is a trifunctional polypeptide. It has phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase activity which is required for de novo purine biosynthesis. This enzyme is highly conserved in vertebrates. Alternative splicing of this gene results in two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

GART 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 (BayesDel_noAF=-0.76).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GART	NM_000819.5 link	c.2841+11C>G		intron_variant	Intron 21 of 21	ENST00000381815.9	NP_000810.1	P22102-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
GART	ENST00000381815.9 link	c.2841+11C>G	intron_variant	Intron 21 of 21	1	NM_000819.5	ENSP00000371236.4	P22102-1
GART	ENST00000381831.7 link	c.2841+11C>G	intron_variant	Intron 21 of 21	1		ENSP00000371253.3	P22102-1
GART	ENST00000381839.7 link	c.2841+11C>G	intron_variant	Intron 21 of 21	1		ENSP00000371261.3	P22102-1
GART	ENST00000424203.5 link	n.*1924+11C>G	intron_variant	Intron 21 of 21	1		ENSP00000390003.1	F8WD69

Frequencies

GnomAD3 genomes

AF:

0.0920

AC:

13995

AN:

152050

Hom.:

887

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0218

Gnomad AMI

AF:

0.0318

Gnomad AMR

AF:

0.149

Gnomad ASJ

AF:

0.119

Gnomad EAS

AF:

0.253

Gnomad SAS

AF:

0.118

Gnomad FIN

AF:

0.127

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.102

Gnomad OTH

AF:

0.0890

GnomAD3 exomes

AF:

0.130

AC:

32725

AN:

251114

Hom.:

2696

AF XY:

0.126

AC XY:

17150

AN XY:

135748

show subpopulations

Gnomad AFR exome

AF:

0.0191

Gnomad AMR exome

AF:

0.227

Gnomad ASJ exome

AF:

0.104

Gnomad EAS exome

AF:

0.248

Gnomad SAS exome

AF:

0.120

Gnomad FIN exome

AF:

0.132

Gnomad NFE exome

AF:

0.104

Gnomad OTH exome

AF:

0.112

GnomAD4 exome

AF:

0.108

AC:

157239

AN:

1458530

Hom.:

9677

Cov.:

AF XY:

0.108

AC XY:

78317

AN XY:

725274

show subpopulations

Gnomad4 AFR exome

AF:

0.0171

Gnomad4 AMR exome

AF:

0.219

Gnomad4 ASJ exome

AF:

0.110

Gnomad4 EAS exome

AF:

0.237

Gnomad4 SAS exome

AF:

0.116

Gnomad4 FIN exome

AF:

0.131

Gnomad4 NFE exome

AF:

0.0996

Gnomad4 OTH exome

AF:

0.107

GnomAD4 genome

AF:

0.0921

AC:

14020

AN:

152168

Hom.:

896

Cov.:

AF XY:

0.0944

AC XY:

7022

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.0217

Gnomad4 AMR

AF:

0.149

Gnomad4 ASJ

AF:

0.119

Gnomad4 EAS

AF:

0.253

Gnomad4 SAS

AF:

0.118

Gnomad4 FIN

AF:

0.127

Gnomad4 NFE

AF:

0.102

Gnomad4 OTH

AF:

0.0975

Alfa

AF:

0.0964

Hom.:

158

Bravo

AF:

0.0942

Asia WGS

AF:

0.197

AC:

686

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

DANN

Benign

0.58

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.12

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