Variant 5-141959206-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000511961.5(RNF14):c.-7+781A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 152,228 control chromosomes in the GnomAD database, including 50,225 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.81 ( 50180 hom., cov: 31)

Exomes 𝑓: 0.85 ( 45 hom. )

Consequence

RNF14
ENST00000511961.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.74

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]

RNF14 links:

PCDH12 (HGNC:):

PCDH12 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 5-141959206-A-G is Benign according to our data. Variant chr5-141959206-A-G is described in ClinVar as [Benign]. Clinvar id is 1294900.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein
RNF14	XM_047417903.1 linkuse as main transcript	c.-181+781A>G	intron_variant	XP_047273859.1
RNF14	XM_047417904.1 linkuse as main transcript	c.-181+9796A>G	intron_variant	XP_047273860.1
RNF14	XM_047417908.1 linkuse as main transcript	c.-181+9796A>G	intron_variant	XP_047273864.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	Protein	UniProt
RNF14	ENST00000511961.5 linkuse as main transcript	c.-7+781A>G	intron_variant	3	ENSP00000423420.1	D6RA38
RNF14	ENST00000506822.5 linkuse as main transcript	c.-181+781A>G	intron_variant	5	ENSP00000423273.1	D6R996
PCDH12	ENST00000512221.2 linkuse as main transcript	n.259-961T>C	intron_variant	3

Frequencies

GnomAD3 genomes

AF:

0.811

AC:

123213

AN:

151984

Hom.:

50155

Cov.:

show subpopulations

Gnomad AFR

AF:

0.796

Gnomad AMI

AF:

0.672

Gnomad AMR

AF:

0.875

Gnomad ASJ

AF:

0.843

Gnomad EAS

AF:

0.993

Gnomad SAS

AF:

0.872

Gnomad FIN

AF:

0.737

Gnomad MID

AF:

0.831

Gnomad NFE

AF:

0.798

Gnomad OTH

AF:

0.816

GnomAD4 exome

AF:

0.849

AC:

107

AN:

126

Hom.:

AF XY:

0.838

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

1.00

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.800

Gnomad4 NFE exome

AF:

0.851

Gnomad4 OTH exome

AF:

1.00

GnomAD4 genome

AF:

0.811

AC:

123297

AN:

152102

Hom.:

50180

Cov.:

AF XY:

0.813

AC XY:

60432

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.796

Gnomad4 AMR

AF:

0.875

Gnomad4 ASJ

AF:

0.843

Gnomad4 EAS

AF:

0.993

Gnomad4 SAS

AF:

0.872

Gnomad4 FIN

AF:

0.737

Gnomad4 NFE

AF:

0.798

Gnomad4 OTH

AF:

0.813

Alfa

AF:

0.810

Hom.:

44106

Bravo

AF:

0.824

Asia WGS

AF:

0.895

AC:

3115

AN:

3478

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 submitter

clinical testing

GeneDx

May 13, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.31

DANN

Benign

0.56

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over