dbSNP rs7264576: PRNT:n.529+3330C>A (chr20-4736810-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000326539.6(PRNT):n.529+3330C>A variant causes a intron 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
ENST00000326539.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.312

Variant links:

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]

PRNT links:

IDI1P3 (HGNC:54668): (IDI1 pseudogene 3)

IDI1P3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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	Effect	Exon rank
PRNT	NR_024267.1 link	n.529+3330C>A	intron_variant	Intron 1 of 1
PRNT	NR_024268.1 link	n.292+3567C>A	intron_variant	Intron 1 of 1
PRNT	NR_024269.1 link	n.70-3725C>A	intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PRNT	ENST00000326539.6 link	n.529+3330C>A	intron_variant	Intron 1 of 1	1
PRNT	ENST00000418528.5 link	n.70-3725C>A	intron_variant	Intron 1 of 1	1
PRNT	ENST00000423718.2 link	n.292+3567C>A	intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes

AF:

0.268

AC:

40757

AN:

151972

Hom.:

5536

Cov.:

show subpopulations

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:

AN:

Hom.:

AF XY:

0.300

AC XY:

AN XY:

show subpopulations

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.:

AF XY:

0.269

AC XY:

20012

AN XY:

74348

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over