5-141982597-A-G

Position:

• chr5-141982597-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004290.5(RNF14):​c.1064-783A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.883 in 152,286 control chromosomes in the GnomAD database, including 59,627 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 0.88 (59625 hom., cov: 33)
  • Exomes 𝑓: 1.0 (2 hom.)
• Consequence: RNF14 NM_004290.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNF14	NM_004290.5	c.1064-783A>G		intron_variant		ENST00000394520.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNF14	ENST00000394520.7	c.1064-783A>G		intron_variant		1	NM_004290.5	P1
	ENST00000520882.1	n.73+18T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.883 AC: 134347 AN: 152164 Hom.: 59564 Cov.: 33

Gnomad AFR AF: 0.953

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.914

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.906

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.842

Gnomad OTH AF: 0.882

GnomAD4 exome AF: 1.00 AC: 4 AN: 4 Hom.: 2 Cov.: 0 AF XY: 1.00 AC XY: 4 AN XY: 4

Gnomad4 FIN exome AF: 1.00

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.883 AC: 134466 AN: 152282 Hom.: 59625 Cov.: 33 AF XY: 0.884 AC XY: 65772 AN XY: 74438

Gnomad4 AFR AF: 0.953

Gnomad4 AMR AF: 0.914

Gnomad4 ASJ AF: 0.832

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.906

Gnomad4 FIN AF: 0.802

Gnomad4 NFE AF: 0.842

Gnomad4 OTH AF: 0.879

Alfa AF: 0.856 Hom.: 24434

Bravo AF: 0.895

Asia WGS AF: 0.926 AC: 3218 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.0
DANN	Benign	0.83

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

Other links and lift over

dbSNP: rs252095; hg19: chr5-141362162;