rs7264576

chr20-4736810-G-T

Variant summary

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

The NR_024269.1(PRNT):n.70-3725C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,116 control chromosomes in the GnomAD database, including 5,548 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 0.27 (5547 hom., cov: 32)
  • Exomes 𝑓: 0.25 (1 hom.)
• Consequence: PRNT NR_024269.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

Genes affected

PRNT (HGNC:18046): (prion locus lncRNA, testis expressed) Predicted to be located in extracellular region. [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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRNT	NR_024269.1	n.70-3725C>A		intron_variant, non_coding_transcript_variant
PRNT	NR_024267.1	n.529+3330C>A		intron_variant, non_coding_transcript_variant
PRNT	NR_024268.1	n.292+3567C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRNT	ENST00000326539.6	n.529+3330C>A		intron_variant, non_coding_transcript_variant		1
PRNT	ENST00000418528.5	n.70-3725C>A		intron_variant, non_coding_transcript_variant		1
PRNT	ENST00000423718.2	n.292+3567C>A		intron_variant, non_coding_transcript_variant		1
PRNT	ENST00000662883.1	n.70+3567C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40757 AN: 151972 Hom.: 5536 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.282

GnomAD4 exome AF: 0.250 AC: 6 AN: 24 Hom.: 1 AF XY: 0.300 AC XY: 6 AN XY: 20

Gnomad4 ASJ exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.333

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.268 AC: 40799 AN: 152092 Hom.: 5547 Cov.: 32 AF XY: 0.269 AC XY: 20012 AN XY: 74348

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.280

Alfa AF: 0.275 Hom.: 2906

Bravo AF: 0.266

Asia WGS AF: 0.288 AC: 1000 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	0.77
Dann	Benign	0.35

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: rs7264576; hg19: chr20-4717456;