Genetic Variant RSBN1:p.Arg31Arg (chr1-113812320-T-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_018364.5(RSBN1):c.93A>C(p.Arg31Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 1,603,660 control chromosomes in the GnomAD database, including 25,635 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 ( 2092 hom., cov: 32)

Exomes 𝑓: 0.18 ( 23543 hom. )

Consequence

RSBN1
NM_018364.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.00

Publications

48 publications found

Variant links:

Genes affected

RSBN1 (HGNC:25642): (round spermatid basic protein 1) Predicted to enable dioxygenase activity and metal ion binding activity. Predicted to be involved in chromatin organization. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

RSBN1 links:

AP4B1-AS1 (HGNC:44114): (AP4B1 antisense RNA 1)

AP4B1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP7

Synonymous conserved (PhyloP=-2 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein
RSBN1	NM_018364.5 link	c.93A>C	p.Arg31Arg	synonymous_variant	Exon 1 of 7	ENST00000261441.9	NP_060834.2
RSBN1	XM_017001518.3 link	c.93A>C	p.Arg31Arg	synonymous_variant	Exon 1 of 3		XP_016857007.1
RSBN1	NR_130896.2 link	n.157A>C		non_coding_transcript_exon_variant	Exon 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RSBN1	ENST00000261441.9 link	c.93A>C	p.Arg31Arg	synonymous_variant	Exon 1 of 7	2	NM_018364.5	ENSP00000261441.5

Frequencies

GnomAD3 genomes

AF:

0.156

AC:

23700

AN:

152106

Hom.:

2091

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0815

Gnomad AMI

AF:

0.231

Gnomad AMR

AF:

0.171

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.229

Gnomad SAS

AF:

0.118

Gnomad FIN

AF:

0.198

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.187

Gnomad OTH

AF:

0.161

GnomAD2 exomes

AF:

0.168

AC:

39434

AN:

234336

AF XY:

0.168

show subpopulations

Gnomad AFR exome

AF:

0.0797

Gnomad AMR exome

AF:

0.139

Gnomad ASJ exome

AF:

0.154

Gnomad EAS exome

AF:

0.231

Gnomad FIN exome

AF:

0.190

Gnomad NFE exome

AF:

0.192

Gnomad OTH exome

AF:

0.169

GnomAD4 exome

AF:

0.178

AC:

257862

AN:

1451436

Hom.:

23543

Cov.:

AF XY:

0.176

AC XY:

127147

AN XY:

722532

show subpopulations

African (AFR)

AF:

0.0735

AC:

2459

AN:

33470

American (AMR)

AF:

0.141

AC:

6318

AN:

44686

Ashkenazi Jewish (ASJ)

AF:

0.153

AC:

4004

AN:

26100

East Asian (EAS)

AF:

0.211

AC:

8360

AN:

39678

South Asian (SAS)

AF:

0.117

AC:

10065

AN:

86218

European-Finnish (FIN)

AF:

0.185

AC:

8051

AN:

43508

Middle Eastern (MID)

AF:

0.120

AC:

690

AN:

5768

European-Non Finnish (NFE)

AF:

0.187

AC:

207580

AN:

1111696

Other (OTH)

AF:

0.171

AC:

10335

AN:

60312

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

13198

26397

39595

52794

65992

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7160

14320

21480

28640

35800

<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:

0.156

AC:

23710

AN:

152224

Hom.:

2092

Cov.:

AF XY:

0.157

AC XY:

11669

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.0816

AC:

3390

AN:

41560

American (AMR)

AF:

0.171

AC:

2610

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.154

AC:

536

AN:

3472

East Asian (EAS)

AF:

0.229

AC:

1181

AN:

5150

South Asian (SAS)

AF:

0.118

AC:

568

AN:

4824

European-Finnish (FIN)

AF:

0.198

AC:

2099

AN:

10616

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.187

AC:

12735

AN:

67996

Other (OTH)

AF:

0.165

AC:

347

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1027

2054

3081

4108

5135

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:

0.173

Hom.:

3241

Bravo

AF:

0.152

Asia WGS

AF:

0.191

AC:

664

AN:

3478

EpiCase

AF:

0.180

EpiControl

AF:

0.189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

5.6

(source)

DANN

Benign

0.54

PhyloP100

-2.0

PromoterAI

0.073

Neutral

(source)

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over