dbSNP rs433623: RNF14:c.*543G>A (chr5-141988333-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004290.5(RNF14):c.*543G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 152,498 control chromosomes in the GnomAD database, including 23,875 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 ( 23775 hom., cov: 32)

Exomes 𝑓: 0.60 ( 100 hom. )

Consequence

RNF14
NM_004290.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.357

Publications

15 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNF14	NM_004290.5 link	c.*543G>A		3_prime_UTR_variant	Exon 9 of 9	ENST00000394520.7	NP_004281.1	Q9UBS8-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF14	ENST00000394520.7 link	c.*543G>A		3_prime_UTR_variant	Exon 9 of 9	1	NM_004290.5	ENSP00000378028.2		Q9UBS8-1

Frequencies

GnomAD3 genomes

AF:

0.538

AC:

81739

AN:

151856

Hom.:

23770

Cov.:

show subpopulations

Gnomad AFR

AF:

0.334

Gnomad AMI

AF:

0.496

Gnomad AMR

AF:

0.684

Gnomad ASJ

AF:

0.620

Gnomad EAS

AF:

0.977

Gnomad SAS

AF:

0.725

Gnomad FIN

AF:

0.571

Gnomad MID

AF:

0.630

Gnomad NFE

AF:

0.573

Gnomad OTH

AF:

0.571

GnomAD4 exome

AF:

0.599

AC:

314

AN:

524

Hom.:

100

Cov.:

AF XY:

0.599

AC XY:

182

AN XY:

304

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.703

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.600

AC:

AN:

140

South Asian (SAS)

AF:

0.679

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.574

AC:

162

AN:

282

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.532

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.538

AC:

81766

AN:

151974

Hom.:

23775

Cov.:

AF XY:

0.546

AC XY:

40523

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.334

AC:

13829

AN:

41434

American (AMR)

AF:

0.685

AC:

10465

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.620

AC:

2151

AN:

3472

East Asian (EAS)

AF:

0.977

AC:

5053

AN:

5170

South Asian (SAS)

AF:

0.726

AC:

3501

AN:

4822

European-Finnish (FIN)

AF:

0.571

AC:

6023

AN:

10540

Middle Eastern (MID)

AF:

0.622

AC:

183

AN:

294

European-Non Finnish (NFE)

AF:

0.573

AC:

38907

AN:

67936

Other (OTH)

AF:

0.570

AC:

1202

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1780

3559

5339

7118

8898

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

708

1416

2124

2832

3540

<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:

0.563

Hom.:

64296

Bravo

AF:

0.538

Asia WGS

AF:

0.772

AC:

2679

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.59

(source)

DANN

Benign

0.68

PhyloP100

-0.36

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(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

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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