rs11014306

chr10-24935533-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020200.7(PRTFDC1):c.339+1651A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,116 control chromosomes in the GnomAD database, including 4,654 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 0.20 (4654 hom., cov: 32)
• Consequence: PRTFDC1 NM_020200.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835

Genes affected

PRTFDC1 (HGNC:23333): (phosphoribosyl transferase domain containing 1) Enables protein homodimerization activity. Predicted to be involved in purine ribonucleoside salvage. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRTFDC1	NM_020200.7	c.339+1651A>G		intron_variant		ENST00000320152.11
PRTFDC1	NM_001282786.2	c.339+1651A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRTFDC1	ENST00000320152.11	c.339+1651A>G		intron_variant		1	NM_020200.7	P1
PRTFDC1	ENST00000376376.3	c.339+1651A>G		intron_variant		2
PRTFDC1	ENST00000376378.5	c.339+1651A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30589 AN: 151998 Hom.: 4648 Cov.: 32

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0918

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0555

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.177

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.201 AC: 30607 AN: 152116 Hom.: 4654 Cov.: 32 AF XY: 0.196 AC XY: 14582 AN XY: 74384

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.0914

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.0555

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.175

Alfa AF: 0.137 Hom.: 1734

Bravo AF: 0.219

Asia WGS AF: 0.108 AC: 377 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	0.063
Dann	Benign	0.54

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: rs11014306; hg19: chr10-25224462;