dbSNP rs12029359: RPRD2:c.1411+9G>A (chr1-150460326-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_015203.5(RPRD2):c.1411+9G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 1,600,990 control chromosomes in the GnomAD database, including 32,685 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 0.16 ( 2439 hom., cov: 31)

Exomes 𝑓: 0.20 ( 30246 hom. )

Consequence

RPRD2
NM_015203.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0420

Publications

14 publications found

Variant links:

Genes affected

RPRD2 (HGNC:29039): (regulation of nuclear pre-mRNA domain containing 2) Predicted to enable RNA polymerase II complex binding activity. Predicted to be involved in mRNA 3'-end processing. Part of RNA polymerase II, holoenzyme. [provided by Alliance of Genome Resources, Apr 2022]

RPRD2 links:

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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=-0.7).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015203.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
RPRD2	NM_015203.5	MANE Select	c.1411+9G>A	intron	N/A	NP_056018.2	Q5VT52-1
RPRD2	NM_001297674.2		c.1333+9G>A	intron	N/A	NP_001284603.1	Q5VT52-3
RPRD2	NM_001387119.1		c.1411+9G>A	intron	N/A	NP_001374048.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
RPRD2	ENST00000369068.5	TSL:1 MANE Select	c.1411+9G>A	intron	N/A	ENSP00000358064.4	Q5VT52-1
RPRD2	ENST00000401000.8	TSL:1	c.1333+9G>A	intron	N/A	ENSP00000383785.4	Q5VT52-3
RPRD2	ENST00000879565.1		c.1411+9G>A	intron	N/A	ENSP00000549624.1

Frequencies

GnomAD3 genomes

AF:

0.164

AC:

24921

AN:

152098

Hom.:

2437

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0539

Gnomad AMI

AF:

0.228

Gnomad AMR

AF:

0.157

Gnomad ASJ

AF:

0.310

Gnomad EAS

AF:

0.182

Gnomad SAS

AF:

0.211

Gnomad FIN

AF:

0.236

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.207

Gnomad OTH

AF:

0.198

GnomAD2 exomes

AF:

0.189

AC:

44319

AN:

234696

AF XY:

0.196

show subpopulations

Gnomad AFR exome

AF:

0.0471

Gnomad AMR exome

AF:

0.110

Gnomad ASJ exome

AF:

0.316

Gnomad EAS exome

AF:

0.158

Gnomad FIN exome

AF:

0.238

Gnomad NFE exome

AF:

0.208

Gnomad OTH exome

AF:

0.210

GnomAD4 exome

AF:

0.200

AC:

290173

AN:

1448774

Hom.:

30246

Cov.:

AF XY:

0.203

AC XY:

146024

AN XY:

719846

show subpopulations

African (AFR)

AF:

0.0458

AC:

1528

AN:

33338

American (AMR)

AF:

0.112

AC:

4827

AN:

43116

Ashkenazi Jewish (ASJ)

AF:

0.310

AC:

8010

AN:

25816

East Asian (EAS)

AF:

0.178

AC:

7045

AN:

39530

South Asian (SAS)

AF:

0.216

AC:

18408

AN:

85036

European-Finnish (FIN)

AF:

0.236

AC:

12524

AN:

52962

Middle Eastern (MID)

AF:

0.230

AC:

1318

AN:

5740

European-Non Finnish (NFE)

AF:

0.203

AC:

224231

AN:

1103300

Other (OTH)

AF:

0.205

AC:

12282

AN:

59936

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

11105

22211

33316

44422

55527

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7688

15376

23064

30752

38440

<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:

0.164

AC:

24932

AN:

152216

Hom.:

2439

Cov.:

AF XY:

0.165

AC XY:

12305

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.0538

AC:

2236

AN:

41558

American (AMR)

AF:

0.157

AC:

2400

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.310

AC:

1075

AN:

3470

East Asian (EAS)

AF:

0.183

AC:

949

AN:

5188

South Asian (SAS)

AF:

0.212

AC:

1024

AN:

4824

European-Finnish (FIN)

AF:

0.236

AC:

2497

AN:

10582

Middle Eastern (MID)

AF:

0.231

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.207

AC:

14054

AN:

67998

Other (OTH)

AF:

0.199

AC:

422

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1030

2061

3091

4122

5152

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

274

548

822

1096

1370

<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:

0.201

Hom.:

4431

Bravo

AF:

0.154

Asia WGS

AF:

0.230

AC:

800

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

8.9

(source)

DANN

Benign

0.67

PhyloP100

-0.042

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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