dbSNP rs2272040: PRR27:n.98-62A>G (chr4-70141330-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000502441.2(PRR27):n.98-62A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 400,876 control chromosomes in the GnomAD database, including 3,858 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 0.12 ( 1269 hom., cov: 32)

Exomes 𝑓: 0.14 ( 2589 hom. )

Consequence

PRR27
ENST00000502441.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.37

Publications

4 publications found

Variant links:

Genes affected

PRR27 (HGNC:33193): (proline rich 27) Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

PRR27 links:

ENSG00000310584 (HGNC:):

ENSG00000310584 links:

CSN1S2BP (HGNC:20227): (casein alpha s2 like B, pseudogene) This locus is found in a cluster of casein genes, similar to other mammals. In human, the potential open reading frame that matches the homologous protein from other species is prematurely truncated shortly after the signal peptide. Therefore, this locus appears to be a pseudogene. [provided by RefSeq, Feb 2010]

CSN1S2BP links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000502441.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502441.2. 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
	CSN1S2BP	NR_033311.1		n.110-62A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRR27	ENST00000502441.2	TSL:3	n.98-62A>G		intron	N/A
	ENSG00000310584	ENST00000851010.1		n.199-62A>G		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.116

AC:

17673

AN:

151972

Hom.:

1268

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0464

Gnomad AMI

AF:

0.134

Gnomad AMR

AF:

0.173

Gnomad ASJ

AF:

0.209

Gnomad EAS

AF:

0.195

Gnomad SAS

AF:

0.136

Gnomad FIN

AF:

0.0852

Gnomad MID

AF:

0.201

Gnomad NFE

AF:

0.137

Gnomad OTH

AF:

0.166

GnomAD4 exome

AF:

0.139

AC:

34459

AN:

248786

Hom.:

2589

AF XY:

0.140

AC XY:

20119

AN XY:

143768

show subpopulations

African (AFR)

AF:

0.0450

AC:

265

AN:

5886

American (AMR)

AF:

0.170

AC:

2401

AN:

14140

Ashkenazi Jewish (ASJ)

AF:

0.213

AC:

1594

AN:

7494

East Asian (EAS)

AF:

0.197

AC:

1746

AN:

8862

South Asian (SAS)

AF:

0.143

AC:

6945

AN:

48490

European-Finnish (FIN)

AF:

0.0830

AC:

873

AN:

10516

Middle Eastern (MID)

AF:

0.185

AC:

165

AN:

894

European-Non Finnish (NFE)

AF:

0.134

AC:

18834

AN:

140850

Other (OTH)

AF:

0.140

AC:

1636

AN:

11654

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1378

2757

4135

5514

6892

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

140

280

420

560

700

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.116

AC:

17678

AN:

152090

Hom.:

1269

Cov.:

AF XY:

0.116

AC XY:

8647

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.0463

AC:

1922

AN:

41518

American (AMR)

AF:

0.173

AC:

2637

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.209

AC:

724

AN:

3468

East Asian (EAS)

AF:

0.195

AC:

1008

AN:

5170

South Asian (SAS)

AF:

0.138

AC:

664

AN:

4822

European-Finnish (FIN)

AF:

0.0852

AC:

900

AN:

10558

Middle Eastern (MID)

AF:

0.205

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.137

AC:

9291

AN:

67976

Other (OTH)

AF:

0.166

AC:

350

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

757

1513

2270

3026

3783

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

202

404

606

808

1010

<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:

0.133

Hom.:

733

Bravo

AF:

0.122

Asia WGS

AF:

0.140

AC:

485

AN:

3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.0090

(source)

DANN

Benign

0.41

PhyloP100

-2.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over