5-141965653-T-C

Position:

• chr5-141965653-T-C

Variant summary

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

The ENST00000511961.5(RNF14):​c.-7+7228T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.884 in 152,286 control chromosomes in the GnomAD database, including 59,784 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 (59784 hom., cov: 33)
• Consequence: RNF14 ENST00000511961.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.511

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]

PCDH12 (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 = 0.957 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNF14	XM_047417903.1	c.-180-5051T>C		intron_variant			XP_047273859.1
RNF14	XM_047417904.1	c.-180-5051T>C		intron_variant			XP_047273860.1
RNF14	XM_047417908.1	c.-180-5051T>C		intron_variant			XP_047273864.1
LOC124901095	XR_007058977.1	n.174-2439A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNF14	ENST00000511961.5	c.-7+7228T>C		intron_variant		3		ENSP00000423420.1
RNF14	ENST00000506822.5	c.-180-5051T>C		intron_variant		5		ENSP00000423273.1
PCDH12	ENST00000512221.2	n.135-2439A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.884 AC: 134503 AN: 152168 Hom.: 59721 Cov.: 33

Gnomad AFR AF: 0.959

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.912

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.980

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.881

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.884 AC: 134624 AN: 152286 Hom.: 59784 Cov.: 33 AF XY: 0.884 AC XY: 65846 AN XY: 74454

Gnomad4 AFR AF: 0.959

Gnomad4 AMR AF: 0.912

Gnomad4 ASJ AF: 0.831

Gnomad4 EAS AF: 0.980

Gnomad4 SAS AF: 0.903

Gnomad4 FIN AF: 0.801

Gnomad4 NFE AF: 0.841

Gnomad4 OTH AF: 0.878

Alfa AF: 0.848 Hom.: 21420

Bravo AF: 0.896

Asia WGS AF: 0.925 AC: 3216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.4
DANN	Benign	0.84

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs252139; hg19: chr5-141345218;