Genetic Variant NM_031277.3:c.1057C>T (chr13-24793163-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

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

The NM_031277.3(RNF17):c.1057C>T(p.Leu353Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 1,613,574 control chromosomes in the GnomAD database, including 53,274 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 0.22 ( 4336 hom., cov: 32)

Exomes 𝑓: 0.25 ( 48938 hom. )

Consequence

RNF17
NM_031277.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.243

Publications

12 publications found

Variant links:

Genes affected

RNF17 (HGNC:10060): (ring finger protein 17) This gene is similar to a mouse gene that encodes a testis-specific protein containing a RING finger domain. Alternatively spliced transcript variants encoding different isoforms have been found. [provided by RefSeq, May 2010]

RNF17 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=-0.86).

BP7

Synonymous conserved (PhyloP=0.243 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNF17	NM_031277.3 link	c.1057C>T	p.Leu353Leu	synonymous_variant	Exon 10 of 36	ENST00000255324.10	NP_112567.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein
RNF17	ENST00000255324.10 link	c.1057C>T	p.Leu353Leu	synonymous_variant	Exon 10 of 36	2	NM_031277.3	ENSP00000255324.5
RNF17	ENST00000255325.6 link	c.1057C>T	p.Leu353Leu	synonymous_variant	Exon 10 of 15	2		ENSP00000255325.6
RNF17	ENST00000255326.4 link	n.1060C>T		non_coding_transcript_exon_variant	Exon 10 of 12	2

Frequencies

GnomAD3 genomes

AF:

0.223

AC:

33969

AN:

152000

Hom.:

4324

Cov.:

show subpopulations

Gnomad AFR

AF:

0.112

Gnomad AMI

AF:

0.144

Gnomad AMR

AF:

0.316

Gnomad ASJ

AF:

0.289

Gnomad EAS

AF:

0.396

Gnomad SAS

AF:

0.307

Gnomad FIN

AF:

0.311

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.236

Gnomad OTH

AF:

0.224

GnomAD2 exomes

AF:

0.275

AC:

69207

AN:

251298

AF XY:

0.273

show subpopulations

Gnomad AFR exome

AF:

0.107

Gnomad AMR exome

AF:

0.382

Gnomad ASJ exome

AF:

0.292

Gnomad EAS exome

AF:

0.378

Gnomad FIN exome

AF:

0.300

Gnomad NFE exome

AF:

0.233

Gnomad OTH exome

AF:

0.264

GnomAD4 exome

AF:

0.252

AC:

368754

AN:

1461456

Hom.:

48938

Cov.:

AF XY:

0.254

AC XY:

184703

AN XY:

727046

show subpopulations

African (AFR)

AF:

0.109

AC:

3635

AN:

33468

American (AMR)

AF:

0.373

AC:

16668

AN:

44704

Ashkenazi Jewish (ASJ)

AF:

0.288

AC:

7530

AN:

26126

East Asian (EAS)

AF:

0.436

AC:

17290

AN:

39688

South Asian (SAS)

AF:

0.316

AC:

27216

AN:

86230

European-Finnish (FIN)

AF:

0.296

AC:

15810

AN:

53412

Middle Eastern (MID)

AF:

0.239

AC:

1378

AN:

5768

European-Non Finnish (NFE)

AF:

0.238

AC:

264210

AN:

1111678

Other (OTH)

AF:

0.249

AC:

15017

AN:

60382

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

15195

30390

45586

60781

75976

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9230

18460

27690

36920

46150

<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:

0.224

AC:

34010

AN:

152118

Hom.:

4336

Cov.:

AF XY:

0.232

AC XY:

17248

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.112

AC:

4665

AN:

41542

American (AMR)

AF:

0.317

AC:

4844

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.289

AC:

1003

AN:

3472

East Asian (EAS)

AF:

0.397

AC:

2048

AN:

5164

South Asian (SAS)

AF:

0.306

AC:

1473

AN:

4812

European-Finnish (FIN)

AF:

0.311

AC:

3289

AN:

10568

Middle Eastern (MID)

AF:

0.245

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.236

AC:

16015

AN:

67974

Other (OTH)

AF:

0.223

AC:

470

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1320

2639

3959

5278

6598

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

368

736

1104

1472

1840

<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:

0.225

Hom.:

4507

Bravo

AF:

0.217

Asia WGS

AF:

0.314

AC:

1089

AN:

3478

EpiCase

AF:

0.227

EpiControl

AF:

0.224

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.5

(source)

DANN

Benign

0.31

PhyloP100

0.24

Mutation Taster

=98/2

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.14

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