rs79444047

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001146227.3(RPS20):c.343T>C(p.Ser115Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00578 in 1,495,880 control chromosomes in the GnomAD database, including 178 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.019 ( 79 hom., cov: 32)

Exomes 𝑓: 0.0042 ( 99 hom. )

Consequence

RPS20
NM_001146227.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 0.347

Publications

1 publications found

Variant links:

Genes affected

RPS20 (HGNC:10405): (ribosomal protein S20) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 40S subunit. The protein belongs to the S10P family of ribosomal proteins. It is located in the cytoplasm. This gene is co-transcribed with the small nucleolar RNA gene U54, which is located in its second intron. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Two transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Apr 2009]

RPS20 Gene-Disease associations (from GenCC):

Diamond-Blackfan anemia
Inheritance: AD Classification: MODERATE, SUPPORTIVE, LIMITED Submitted by: PanelApp Australia, Orphanet, Ambry Genetics
familial colorectal cancer
Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
familial colorectal cancer type X
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
hereditary nonpolyposis colon cancer
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
Lynch syndrome
Inheritance: AD Classification: LIMITED Submitted by: ClinGen

RPS20 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0018868148).

BP6

Variant 8-56069824-A-G is Benign according to our data. Variant chr8-56069824-A-G is described in ClinVar as Benign. ClinVar VariationId is 1232012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0584 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001146227.3. 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
	RPS20	NM_001146227.3		c.343T>C	p.Ser115Pro	missense	Exon 5 of 6	NP_001139699.1	P60866-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
RPS20	ENST00000519807.5	TSL:2	c.343T>C	p.Ser115Pro	missense	Exon 5 of 6	ENSP00000429374.1	P60866-2
RPS20	ENST00000618656.2	TSL:3	c.325T>C	p.Ser109Pro	missense	Exon 4 of 5	ENSP00000478703.2	A0A7P0S5H5
RPS20	ENST00000676918.1		n.*3266T>C		non_coding_transcript_exon	Exon 4 of 5	ENSP00000503327.1	P60866-1

Frequencies

GnomAD3 genomes

AF:

0.0194

AC:

2955

AN:

152118

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0602

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0102

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.0179

Gnomad SAS

AF:

0.00642

Gnomad FIN

AF:

0.0000943

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00190

Gnomad OTH

AF:

0.0196

GnomAD2 exomes

AF:

0.00785

AC:

1209

AN:

153948

AF XY:

0.00747

show subpopulations

Gnomad AFR exome

AF:

0.0699

Gnomad AMR exome

AF:

0.00652

Gnomad ASJ exome

AF:

0.00330

Gnomad EAS exome

AF:

0.0151

Gnomad FIN exome

AF:

0.0000656

Gnomad NFE exome

AF:

0.00233

Gnomad OTH exome

AF:

0.00600

GnomAD4 exome

AF:

0.00423

AC:

5681

AN:

1343644

Hom.:

Cov.:

AF XY:

0.00416

AC XY:

2769

AN XY:

665856

show subpopulations

African (AFR)

AF:

0.0640

AC:

1953

AN:

30504

American (AMR)

AF:

0.00688

AC:

245

AN:

35628

Ashkenazi Jewish (ASJ)

AF:

0.00375

AC:

AN:

24800

East Asian (EAS)

AF:

0.0226

AC:

800

AN:

35470

South Asian (SAS)

AF:

0.00573

AC:

447

AN:

78032

European-Finnish (FIN)

AF:

0.000102

AC:

AN:

49238

Middle Eastern (MID)

AF:

0.0114

AC:

AN:

5590

European-Non Finnish (NFE)

AF:

0.00161

AC:

1659

AN:

1028306

Other (OTH)

AF:

0.00740

AC:

415

AN:

56076

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

294

587

881

1174

1468

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

112

224

336

448

560

<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:

0.0195

AC:

2964

AN:

152236

Hom.:

Cov.:

AF XY:

0.0192

AC XY:

1429

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.0604

AC:

2507

AN:

41538

American (AMR)

AF:

0.0101

AC:

154

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.00202

AC:

AN:

3472

East Asian (EAS)

AF:

0.0179

AC:

AN:

5188

South Asian (SAS)

AF:

0.00601

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.0000943

AC:

AN:

10606

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00190

AC:

129

AN:

68008

Other (OTH)

AF:

0.0194

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

144

288

433

577

721

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

150

<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:

0.0124

Hom.:

Bravo

AF:

0.0221

TwinsUK

AF:

0.00135

AC:

ALSPAC

AF:

0.000778

AC:

ESP6500AA

AF:

0.0665

AC:

ESP6500EA

AF:

0.00157

AC:

ExAC

AF:

0.0109

AC:

240

Asia WGS

AF:

0.0130

AC:

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

not specified (2)

Familial colorectal cancer type X (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.35

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.66

CADD

Benign

3.3

(source)

DANN

Benign

0.75

Eigen

Benign

-0.93

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.019

LIST_S2

Benign

0.58

MetaRNN

Benign

0.0019

MetaSVM

Benign

-1.1

PhyloP100

0.35

PrimateAI

Benign

0.44

PROVEAN

Benign

-0.49

REVEL

Benign

0.037

Sift

Benign

0.14

Sift4G

Benign

0.14

Vest4

0.17

MPC

1.4

ClinPred

0.0030

GERP RS

0.81

gMVP

0.66

Mutation Taster

=96/4

polymorphism (auto)

(source)

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over