Genetic Variant ENST00000549419.6:n.153-94386G>A (chr12-69998805-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000549419.6(PRANCR):n.153-94386G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 151,984 control chromosomes in the GnomAD database, including 9,833 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 0.35 ( 9833 hom., cov: 32)

Consequence

PRANCR
ENST00000549419.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.11

Publications

2 publications found

Variant links:

Genes affected

PRANCR (HGNC:51126): (progenitor renewal associated non-coding RNA)

PRANCR links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRANCR	ENST00000549419.6 link	n.153-94386G>A		intron_variant	Intron 2 of 2	4
PRANCR	ENST00000668518.1 link	n.370-94386G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.350

AC:

53182

AN:

151866

Hom.:

9837

Cov.:

show subpopulations

Gnomad AFR

AF:

0.229

Gnomad AMI

AF:

0.301

Gnomad AMR

AF:

0.353

Gnomad ASJ

AF:

0.306

Gnomad EAS

AF:

0.393

Gnomad SAS

AF:

0.315

Gnomad FIN

AF:

0.371

Gnomad MID

AF:

0.261

Gnomad NFE

AF:

0.422

Gnomad OTH

AF:

0.365

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

GnomAD4 genome

AF:

0.350

AC:

53184

AN:

151984

Hom.:

9833

Cov.:

AF XY:

0.344

AC XY:

25580

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.229

AC:

9499

AN:

41470

American (AMR)

AF:

0.353

AC:

5395

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.306

AC:

1063

AN:

3470

East Asian (EAS)

AF:

0.392

AC:

2025

AN:

5160

South Asian (SAS)

AF:

0.314

AC:

1510

AN:

4802

European-Finnish (FIN)

AF:

0.371

AC:

3919

AN:

10554

Middle Eastern (MID)

AF:

0.253

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.422

AC:

28662

AN:

67936

Other (OTH)

AF:

0.363

AC:

764

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1708

3417

5125

6834

8542

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

524

1048

1572

2096

2620

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.395

Hom.:

51534

Bravo

AF:

0.347

Asia WGS

AF:

0.357

AC:

1242

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.11

(source)

DANN

Benign

0.37

PhyloP100

-1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over