4-56412149-A-T

Variant summary

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

The ENST00000264220.6(PPAT):​c.129-4433T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 151,940 control chromosomes in the GnomAD database, including 35,347 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 0.68 ( 35347 hom., cov: 30)

Consequence

PPAT
ENST00000264220.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.12
Variant links:
Genes affected
PPAT (HGNC:9238): (phosphoribosyl pyrophosphate amidotransferase) The protein encoded by this gene is a member of the purine/pyrimidine phosphoribosyltransferase family. It is a regulatory allosteric enzyme that catalyzes the first step of de novo purine nucleotide biosythetic pathway. This gene and PAICS/AIRC gene, a bifunctional enzyme catalyzing steps six and seven of this pathway, are located in close proximity on chromosome 4, and divergently transcribed from an intergenic region. [provided by RefSeq, Mar 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PPATNM_002703.5 linkuse as main transcriptc.129-4433T>A intron_variant ENST00000264220.6 NP_002694.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PPATENST00000264220.6 linkuse as main transcriptc.129-4433T>A intron_variant 1 NM_002703.5 ENSP00000264220 P1
ENST00000635939.1 linkuse as main transcriptn.256+1252A>T intron_variant, non_coding_transcript_variant 2
ENST00000636730.1 linkuse as main transcriptn.382+1252A>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.681
AC:
103401
AN:
151822
Hom.:
35320
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.662
Gnomad AMI
AF:
0.605
Gnomad AMR
AF:
0.758
Gnomad ASJ
AF:
0.595
Gnomad EAS
AF:
0.708
Gnomad SAS
AF:
0.726
Gnomad FIN
AF:
0.752
Gnomad MID
AF:
0.608
Gnomad NFE
AF:
0.665
Gnomad OTH
AF:
0.667
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.681
AC:
103479
AN:
151940
Hom.:
35347
Cov.:
30
AF XY:
0.687
AC XY:
51032
AN XY:
74292
show subpopulations
Gnomad4 AFR
AF:
0.662
Gnomad4 AMR
AF:
0.759
Gnomad4 ASJ
AF:
0.595
Gnomad4 EAS
AF:
0.707
Gnomad4 SAS
AF:
0.727
Gnomad4 FIN
AF:
0.752
Gnomad4 NFE
AF:
0.665
Gnomad4 OTH
AF:
0.662
Alfa
AF:
0.668
Hom.:
4198
Bravo
AF:
0.680
Asia WGS
AF:
0.707
AC:
2461
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.092
DANN
Benign
0.75

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.

Other links and lift over

dbSNP: rs9683679; hg19: chr4-57278315; API