rs9302998

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000269391.11(RNF157):​c.89-3306C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 152,042 control chromosomes in the GnomAD database, including 23,951 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 0.54 ( 23951 hom., cov: 32)

Consequence

RNF157
ENST00000269391.11 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.365
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RNF157NM_052916.3 linkuse as main transcriptc.89-3306C>T intron_variant ENST00000269391.11 NP_443148.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RNF157ENST00000269391.11 linkuse as main transcriptc.89-3306C>T intron_variant 1 NM_052916.3 ENSP00000269391 P4Q96PX1-1
RNF157ENST00000319945.10 linkuse as main transcriptc.89-3306C>T intron_variant 2 ENSP00000321837 Q96PX1-2
RNF157ENST00000592271.1 linkuse as main transcriptc.89-3306C>T intron_variant 2 ENSP00000465543
RNF157ENST00000647930.1 linkuse as main transcriptc.89-3306C>T intron_variant ENSP00000497353 A1

Frequencies

GnomAD3 genomes
AF:
0.543
AC:
82422
AN:
151922
Hom.:
23904
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.757
Gnomad AMI
AF:
0.464
Gnomad AMR
AF:
0.502
Gnomad ASJ
AF:
0.444
Gnomad EAS
AF:
0.501
Gnomad SAS
AF:
0.424
Gnomad FIN
AF:
0.456
Gnomad MID
AF:
0.424
Gnomad NFE
AF:
0.453
Gnomad OTH
AF:
0.538
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.543
AC:
82526
AN:
152042
Hom.:
23951
Cov.:
32
AF XY:
0.541
AC XY:
40193
AN XY:
74330
show subpopulations
Gnomad4 AFR
AF:
0.757
Gnomad4 AMR
AF:
0.502
Gnomad4 ASJ
AF:
0.444
Gnomad4 EAS
AF:
0.500
Gnomad4 SAS
AF:
0.426
Gnomad4 FIN
AF:
0.456
Gnomad4 NFE
AF:
0.453
Gnomad4 OTH
AF:
0.538
Alfa
AF:
0.467
Hom.:
28054
Bravo
AF:
0.556
Asia WGS
AF:
0.456
AC:
1587
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
4.9
DANN
Benign
0.63

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9302998; hg19: chr17-74211869; API