rs61751845

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_052916.3(RNF157):c.1391C>T(p.Pro464Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0107 in 1,612,554 control chromosomes in the GnomAD database, including 124 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0076 ( 8 hom., cov: 32)

Exomes 𝑓: 0.011 ( 116 hom. )

Consequence

RNF157
NM_052916.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.277

Publications

8 publications found

Variant links:

Genes affected

RNF157 (HGNC:29402): (ring finger protein 157) Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in several processes, including negative regulation of signal transduction; positive regulation of dendrite extension; and protein autoubiquitination. Predicted to be located in cell body. Predicted to be active in early endosome; nucleus; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

RNF157 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004362017).

BP6

Variant 17-76158415-G-A is Benign according to our data. Variant chr17-76158415-G-A is described in ClinVar as [Benign]. Clinvar id is 791506.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNF157	NM_052916.3 link	c.1391C>T	p.Pro464Leu	missense_variant	Exon 13 of 19	ENST00000269391.11	NP_443148.1	Q96PX1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
RNF157	ENST00000269391.11 link	c.1391C>T	p.Pro464Leu	missense_variant	Exon 13 of 19	1	NM_052916.3	ENSP00000269391.4	Q96PX1-1
RNF157	ENST00000647930.1 link	c.1391C>T	p.Pro464Leu	missense_variant	Exon 13 of 19			ENSP00000497353.1	A0A3B3ISM3
RNF157	ENST00000319945.10 link	c.1391C>T	p.Pro464Leu	missense_variant	Exon 13 of 18	2		ENSP00000321837.4	Q96PX1-2
RNF157	ENST00000592869.1 link	n.109C>T		non_coding_transcript_exon_variant	Exon 1 of 5	4

Frequencies

GnomAD3 genomes

AF:

0.00757

AC:

1152

AN:

152088

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00220

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00367

Gnomad ASJ

AF:

0.0130

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.00821

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0126

Gnomad OTH

AF:

0.00527

GnomAD2 exomes

AF:

0.00729

AC:

1832

AN:

251160

AF XY:

0.00700

show subpopulations

Gnomad AFR exome

AF:

0.00179

Gnomad AMR exome

AF:

0.00226

Gnomad ASJ exome

AF:

0.0108

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00772

Gnomad NFE exome

AF:

0.0119

Gnomad OTH exome

AF:

0.00814

GnomAD4 exome

AF:

0.0110

AC:

16124

AN:

1460348

Hom.:

116

Cov.:

AF XY:

0.0106

AC XY:

7682

AN XY:

726570

show subpopulations

African (AFR)

AF:

0.00173

AC:

AN:

33466

American (AMR)

AF:

0.00259

AC:

116

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.0111

AC:

289

AN:

26130

East Asian (EAS)

AF:

0.00

AC:

AN:

39690

South Asian (SAS)

AF:

0.00168

AC:

145

AN:

86224

European-Finnish (FIN)

AF:

0.00774

AC:

412

AN:

53220

Middle Eastern (MID)

AF:

0.000867

AC:

AN:

5766

European-Non Finnish (NFE)

AF:

0.0131

AC:

14510

AN:

1110784

Other (OTH)

AF:

0.00976

AC:

589

AN:

60348

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

707

1415

2122

2830

3537

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.00757

AC:

1152

AN:

152206

Hom.:

Cov.:

AF XY:

0.00690

AC XY:

513

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.00219

AC:

AN:

41540

American (AMR)

AF:

0.00366

AC:

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0130

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5174

South Asian (SAS)

AF:

0.00146

AC:

AN:

4808

European-Finnish (FIN)

AF:

0.00821

AC:

AN:

10592

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0126

AC:

855

AN:

68018

Other (OTH)

AF:

0.00521

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

121

181

242

302

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00951

Hom.:

Bravo

AF:

0.00723

TwinsUK

AF:

0.0151

AC:

ALSPAC

AF:

0.0104

AC:

ESP6500AA

AF:

0.00204

AC:

ESP6500EA

AF:

0.0123

AC:

106

ExAC

AF:

0.00739

AC:

897

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.0107

EpiControl

AF:

0.00960

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Jul 06, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.065

BayesDel_addAF

Benign

-0.70

BayesDel_noAF

Benign

-0.76

CADD

Benign

1.9

(source)

DANN

Benign

0.64

DEOGEN2

Benign

0.0058

T;.;.

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.046

LIST_S2

Benign

0.71

T;T;T

MetaRNN

Benign

0.0044

T;T;T

MetaSVM

Benign

-0.97

MutationAssessor

Benign

-0.34

N;.;N

PhyloP100

-0.28

PrimateAI

Benign

0.27

PROVEAN

Benign

-1.7

N;.;N

REVEL

Benign

0.022

Sift

Benign

0.38

T;.;T

Sift4G

Benign

0.44

T;.;T

Polyphen

0.0

B;.;B

Vest4

0.11

MVP

0.32

MPC

0.14

ClinPred

0.0013

GERP RS

-0.30

Varity_R

0.025

gMVP

0.19

Mutation Taster

=100/0

polymorphism

(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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

rs61751845

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over