chr4-56394865-A-T

Position:

• chr4-56394865-A-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000264220.6(PPAT):​c.*487T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.45 (4230 hom., cov: 0)
  • Exomes 𝑓: 0.29 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PPAT ENST00000264220.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96

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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPAT	NM_002703.5	c.*487T>A		3_prime_UTR_variant	11/11	ENST00000264220.6	NP_002694.3
PPAT	NR_156493.2	n.2096T>A		non_coding_transcript_exon_variant	11/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPAT	ENST00000264220.6	c.*487T>A		3_prime_UTR_variant	11/11	1	NM_002703.5	ENSP00000264220	P1
PPAT	ENST00000425339.2	n.2543T>A		non_coding_transcript_exon_variant	3/3	1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 33820 AN: 74968 Hom.: 4225 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.359

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.439

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.286 AC: 4 AN: 14 Hom.: 0 Cov.: 0 AF XY: 0.333 AC XY: 4 AN XY: 12

Gnomad4 NFE exome AF: 0.286

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.451 AC: 33855 AN: 75026 Hom.: 4230 Cov.: 0 AF XY: 0.459 AC XY: 16978 AN XY: 37014

Gnomad4 AFR AF: 0.445

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.441

Bravo AF: 0.679

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.84
DANN	Benign	0.20

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

Other links and lift over

dbSNP: rs1042037; hg19: chr4-57261031;