dbSNP rs2236313: RNASET2:c.204-162A>G (chr6-166946901-T-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_003730.6(RNASET2):c.204-162A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 691,096 control chromosomes in the GnomAD database, including 84,511 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 0.50 ( 19706 hom., cov: 32)

Exomes 𝑓: 0.48 ( 64805 hom. )

Consequence

RNASET2
NM_003730.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.233

Publications

48 publications found

Variant links:

Genes affected

RNASET2 (HGNC:21686): (ribonuclease T2) This ribonuclease gene is a novel member of the Rh/T2/S-glycoprotein class of extracellular ribonucleases. It is a single copy gene that maps to 6q27, a region associated with human malignancies and chromosomal rearrangement. [provided by RefSeq, Jul 2008]

RNASET2 Gene-Disease associations (from GenCC):

cystic leukoencephalopathy without megalencephaly
Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae), Illumina, PanelApp Australia, Orphanet

RNASET2 links:

ENSG00000249141 (HGNC:):

ENSG00000249141 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=-0.98).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNASET2	NM_003730.6 link	c.204-162A>G		intron_variant	Intron 3 of 8	ENST00000508775.6	NP_003721.2	O00584-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNASET2	ENST00000508775.6 link	c.204-162A>G		intron_variant	Intron 3 of 8	1	NM_003730.6	ENSP00000426455.2		O00584-1
ENSG00000249141	ENST00000507747.1 link	c.144-162A>G		intron_variant	Intron 3 of 7	5		ENSP00000426906.1		H0YAE9

Frequencies

GnomAD3 genomes

AF:

0.501

AC:

76057

AN:

151910

Hom.:

19674

Cov.:

show subpopulations

Gnomad AFR

AF:

0.586

Gnomad AMI

AF:

0.559

Gnomad AMR

AF:

0.577

Gnomad ASJ

AF:

0.510

Gnomad EAS

AF:

0.621

Gnomad SAS

AF:

0.661

Gnomad FIN

AF:

0.454

Gnomad MID

AF:

0.522

Gnomad NFE

AF:

0.416

Gnomad OTH

AF:

0.520

GnomAD2 exomes

AF:

0.528

AC:

70751

AN:

133926

AF XY:

0.530

show subpopulations

Gnomad AFR exome

AF:

0.598

Gnomad AMR exome

AF:

0.643

Gnomad ASJ exome

AF:

0.509

Gnomad EAS exome

AF:

0.631

Gnomad FIN exome

AF:

0.457

Gnomad NFE exome

AF:

0.415

Gnomad OTH exome

AF:

0.512

GnomAD4 exome

AF:

0.479

AC:

258327

AN:

539068

Hom.:

64805

Cov.:

AF XY:

0.487

AC XY:

142055

AN XY:

291858

show subpopulations

African (AFR)

AF:

0.587

AC:

8650

AN:

14734

American (AMR)

AF:

0.639

AC:

20606

AN:

32232

Ashkenazi Jewish (ASJ)

AF:

0.511

AC:

9929

AN:

19418

East Asian (EAS)

AF:

0.606

AC:

19061

AN:

31478

South Asian (SAS)

AF:

0.656

AC:

39039

AN:

59524

European-Finnish (FIN)

AF:

0.451

AC:

17580

AN:

38996

Middle Eastern (MID)

AF:

0.499

AC:

1452

AN:

2912

European-Non Finnish (NFE)

AF:

0.412

AC:

127703

AN:

310150

Other (OTH)

AF:

0.483

AC:

14307

AN:

29624

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

6912

13824

20736

27648

34560

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

802

1604

2406

3208

4010

<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:

0.501

AC:

76143

AN:

152028

Hom.:

19706

Cov.:

AF XY:

0.508

AC XY:

37741

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.586

AC:

24288

AN:

41436

American (AMR)

AF:

0.577

AC:

8819

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.510

AC:

1769

AN:

3470

East Asian (EAS)

AF:

0.621

AC:

3214

AN:

5176

South Asian (SAS)

AF:

0.662

AC:

3185

AN:

4810

European-Finnish (FIN)

AF:

0.454

AC:

4792

AN:

10560

Middle Eastern (MID)

AF:

0.507

AC:

149

AN:

294

European-Non Finnish (NFE)

AF:

0.416

AC:

28307

AN:

67970

Other (OTH)

AF:

0.525

AC:

1110

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1901

3801

5702

7602

9503

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

686

1372

2058

2744

3430

<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:

0.448

Hom.:

71978

Bravo

AF:

0.515

Asia WGS

AF:

0.650

AC:

2260

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.99

(source)

DANN

Benign

0.47

PhyloP100

-0.23

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