dbSNP rs2233860: RNASE3:c.*16G>C (chr14-20892185-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_002935.3(RNASE3):c.*16G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 1,594,758 control chromosomes in the GnomAD database, including 31,128 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 0.19 ( 3286 hom., cov: 30)

Exomes 𝑓: 0.19 ( 27842 hom. )

Consequence

RNASE3
NM_002935.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.110

Publications

22 publications found

Variant links:

Genes affected

RNASE3 (HGNC:10046): (ribonuclease A family member 3) The protein encoded by this gene belongs to the pancreatic ribonuclease family, a subset of the ribonuclease A superfamily. The protein exhibits antimicrobial activity against pathogenic bacteria [provided by RefSeq, Oct 2014]

RNASE3 links:

ENSG00000259130 (HGNC:):

ENSG00000259130 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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNASE3	NM_002935.3 link	c.*16G>C		3_prime_UTR_variant	Exon 2 of 2	ENST00000304639.4	NP_002926.2	P12724
LOC100507513	XR_110261.4 link	n.723-16442C>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNASE3	ENST00000304639.4 link	c.*16G>C		3_prime_UTR_variant	Exon 2 of 2	1	NM_002935.3	ENSP00000302324.3		P12724

Frequencies

GnomAD3 genomes

AF:

0.191

AC:

28803

AN:

150504

Hom.:

3281

Cov.:

show subpopulations

Gnomad AFR

AF:

0.220

Gnomad AMI

AF:

0.302

Gnomad AMR

AF:

0.149

Gnomad ASJ

AF:

0.208

Gnomad EAS

AF:

0.134

Gnomad SAS

AF:

0.154

Gnomad FIN

AF:

0.151

Gnomad MID

AF:

0.194

Gnomad NFE

AF:

0.195

Gnomad OTH

AF:

0.190

GnomAD2 exomes

AF:

0.177

AC:

41617

AN:

235548

AF XY:

0.180

show subpopulations

Gnomad AFR exome

AF:

0.226

Gnomad AMR exome

AF:

0.0958

Gnomad ASJ exome

AF:

0.223

Gnomad EAS exome

AF:

0.144

Gnomad FIN exome

AF:

0.150

Gnomad NFE exome

AF:

0.202

Gnomad OTH exome

AF:

0.187

GnomAD4 exome

AF:

0.192

AC:

276647

AN:

1444136

Hom.:

27842

Cov.:

AF XY:

0.191

AC XY:

136947

AN XY:

716930

show subpopulations

African (AFR)

AF:

0.220

AC:

7222

AN:

32764

American (AMR)

AF:

0.101

AC:

4357

AN:

43068

Ashkenazi Jewish (ASJ)

AF:

0.215

AC:

5264

AN:

24510

East Asian (EAS)

AF:

0.146

AC:

5781

AN:

39622

South Asian (SAS)

AF:

0.161

AC:

13328

AN:

82828

European-Finnish (FIN)

AF:

0.151

AC:

7911

AN:

52470

Middle Eastern (MID)

AF:

0.208

AC:

1176

AN:

5652

European-Non Finnish (NFE)

AF:

0.200

AC:

220485

AN:

1103608

Other (OTH)

AF:

0.187

AC:

11123

AN:

59614

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

14074

28148

42221

56295

70369

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7678

15356

23034

30712

38390

<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:

0.191

AC:

28819

AN:

150622

Hom.:

3286

Cov.:

AF XY:

0.189

AC XY:

13938

AN XY:

73622

show subpopulations

African (AFR)

AF:

0.219

AC:

8800

AN:

40132

American (AMR)

AF:

0.149

AC:

2270

AN:

15226

Ashkenazi Jewish (ASJ)

AF:

0.208

AC:

721

AN:

3470

East Asian (EAS)

AF:

0.134

AC:

690

AN:

5160

South Asian (SAS)

AF:

0.154

AC:

739

AN:

4810

European-Finnish (FIN)

AF:

0.151

AC:

1590

AN:

10552

Middle Eastern (MID)

AF:

0.195

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.195

AC:

13275

AN:

67964

Other (OTH)

AF:

0.191

AC:

402

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1113

2226

3338

4451

5564

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

316

632

948

1264

1580

<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:

0.191

Hom.:

601

Bravo

AF:

0.195

Asia WGS

AF:

0.130

AC:

453

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.4

(source)

DANN

Benign

0.37

PhyloP100

-0.11

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