chr10-24935533-T-C

Variant names:

• chr10-24935533-T-C
• rs11014306
• NM_020200.7:c.339+1651A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020200.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRTFDC1	NM_020200.7	MANE Select	c.339+1651A>G		intron	N/A	NP_064585.1	Q9NRG1-1
	PRTFDC1	NM_001282786.2		c.339+1651A>G		intron	N/A	NP_001269715.1	Q9NRG1-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRTFDC1	ENST00000320152.11	TSL:1 MANE Select	c.339+1651A>G		intron	N/A	ENSP00000318602.5	Q9NRG1-1
	PRTFDC1	ENST00000897639.1		c.339+1651A>G		intron	N/A	ENSP00000567698.1
	PRTFDC1	ENST00000947509.1		c.288+1651A>G		intron	N/A	ENSP00000617568.1

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

African (AFR) AF: 0.429 AC: 17782 AN: 41442

American (AMR) AF: 0.137 AC: 2092 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 636 AN: 3466

East Asian (EAS) AF: 0.0914 AC: 474 AN: 5184

South Asian (SAS) AF: 0.120 AC: 580 AN: 4820

European-Finnish (FIN) AF: 0.0555 AC: 589 AN: 10608

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7910 AN: 67992

Other (OTH) AF: 0.175 AC: 368 AN: 2106

Alfa AF: 0.150 Hom.: 3351

Bravo AF: 0.219

Asia WGS AF: 0.108 AC: 377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.063
DANN	Benign	0.54
PhyloP100		-0.83
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11014306; hg19: chr10-25224462;