Menu
GeneBe

5-141980347-T-G

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_004290.5(RNF14):c.1059T>G(p.Thr353=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0012 in 1,612,786 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0040 ( 4 hom., cov: 33)
Exomes 𝑓: 0.00091 ( 7 hom. )

Consequence

RNF14
NM_004290.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.711
Variant links:
Genes affected
RNF14 (HGNC:10058): (ring finger protein 14) The protein encoded by this gene contains a RING zinc finger, a motif known to be involved in protein-protein interactions. This protein interacts with androgen receptor (AR) and may function as a coactivator that induces AR target gene expression in prostate. A dominant negative mutant of this gene has been demonstrated to inhibit the AR-mediated growth of prostate cancer. This protein also interacts with class III ubiquitin-conjugating enzymes (E2s) and may act as a ubiquitin-ligase (E3) in the ubiquitination of certain nuclear proteins. Six alternatively spliced transcript variants encoding two distinct isoforms have been reported. [provided by RefSeq, Jan 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 5-141980347-T-G is Benign according to our data. Variant chr5-141980347-T-G is described in ClinVar as [Benign]. Clinvar id is 791533.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.711 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 4 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RNF14NM_004290.5 linkuse as main transcriptc.1059T>G p.Thr353= synonymous_variant 6/9 ENST00000394520.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RNF14ENST00000394520.7 linkuse as main transcriptc.1059T>G p.Thr353= synonymous_variant 6/91 NM_004290.5 P1Q9UBS8-1
ENST00000520882.1 linkuse as main transcriptn.156+1255A>C intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00395
AC:
601
AN:
152244
Hom.:
4
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0118
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00340
Gnomad ASJ
AF:
0.00259
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.0000941
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000632
Gnomad OTH
AF:
0.00287
GnomAD3 exomes
AF:
0.00159
AC:
399
AN:
250724
Hom.:
3
AF XY:
0.00134
AC XY:
182
AN XY:
135602
show subpopulations
Gnomad AFR exome
AF:
0.0135
Gnomad AMR exome
AF:
0.00180
Gnomad ASJ exome
AF:
0.00209
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000131
Gnomad FIN exome
AF:
0.0000468
Gnomad NFE exome
AF:
0.000661
Gnomad OTH exome
AF:
0.00278
GnomAD4 exome
AF:
0.000909
AC:
1327
AN:
1460424
Hom.:
7
Cov.:
30
AF XY:
0.000877
AC XY:
637
AN XY:
726620
show subpopulations
Gnomad4 AFR exome
AF:
0.0137
Gnomad4 AMR exome
AF:
0.00210
Gnomad4 ASJ exome
AF:
0.00287
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000244
Gnomad4 FIN exome
AF:
0.0000378
Gnomad4 NFE exome
AF:
0.000460
Gnomad4 OTH exome
AF:
0.00215
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00396
AC:
603
AN:
152362
Hom.:
4
Cov.:
33
AF XY:
0.00393
AC XY:
293
AN XY:
74512
show subpopulations
Gnomad4 AFR
AF:
0.0118
Gnomad4 AMR
AF:
0.00340
Gnomad4 ASJ
AF:
0.00259
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.0000941
Gnomad4 NFE
AF:
0.000632
Gnomad4 OTH
AF:
0.00284
Alfa
AF:
0.00210
Hom.:
0
Bravo
AF:
0.00479
EpiCase
AF:
0.000818
EpiControl
AF:
0.00107

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeSep 10, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.46
Cadd
Benign
7.2
Dann
Benign
0.70

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs147059342; hg19: chr5-141359912; API