NM_020200.7:c.340-13734G>A

Variant names:

• chr10-24885797-C-T
• rs7078551
• NM_020200.7:c.340-13734G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020200.7(PRTFDC1):​c.340-13734G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,126 control chromosomes in the GnomAD database, including 6,729 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 0.29 (6729 hom., cov: 33)
• Consequence: PRTFDC1 NM_020200.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• Publications: 3 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRTFDC1	NM_020200.7	c.340-13734G>A		intron_variant	Intron 3 of 8	ENST00000320152.11	NP_064585.1
PRTFDC1	NM_001282786.2	c.340-13734G>A		intron_variant	Intron 3 of 7		NP_001269715.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRTFDC1	ENST00000320152.11	c.340-13734G>A		intron_variant	Intron 3 of 8	1	NM_020200.7	ENSP00000318602.5
PRTFDC1	ENST00000376378.5	c.340-13734G>A		intron_variant	Intron 3 of 7	2		ENSP00000365558.1

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44472 AN: 152008 Hom.: 6731 Cov.: 33

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.292 AC: 44495 AN: 152126 Hom.: 6729 Cov.: 33 AF XY: 0.292 AC XY: 21737 AN XY: 74374

African (AFR) AF: 0.235 AC: 9765 AN: 41492

American (AMR) AF: 0.319 AC: 4865 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1130 AN: 3464

East Asian (EAS) AF: 0.200 AC: 1037 AN: 5176

South Asian (SAS) AF: 0.382 AC: 1844 AN: 4824

European-Finnish (FIN) AF: 0.282 AC: 2985 AN: 10578

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21966 AN: 68002

Other (OTH) AF: 0.288 AC: 609 AN: 2116

Alfa AF: 0.298 Hom.: 1127

Bravo AF: 0.288

Asia WGS AF: 0.294 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.32
PhyloP100		0.029
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: rs7078551; hg19: chr10-25174726;