5-141959323-T-C

Variant names:

• chr5-141959323-T-C
• rs252109
• ENST00000511961.5:c.-7+898T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000511961.5(RNF14):​c.-7+898T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.882 in 152,176 control chromosomes in the GnomAD database, including 59,501 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 (59501 hom., cov: 31)
• Consequence: RNF14 ENST00000511961.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35
• Publications: 4 publications found

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:8657): (protocadherin 12) This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. The encoded protein consists of an extracellular domain containing 6 cadherin repeats, a transmembrane domain and a cytoplasmic tail that differs from those of the classical cadherins. The gene localizes to the region on chromosome 5 where the protocadherin gene clusters reside. The exon organization of this transcript is similar to that of the gene cluster transcripts, notably the first large exon, but no significant sequence homology exists. The function of this cellular adhesion protein is undetermined but mouse protocadherin 12 does not bind catenins and appears to have no affect on cell migration or growth. [provided by RefSeq, Jul 2008]

PCDH12 Gene-Disease associations (from GenCC):

• diencephalic-mesencephalic junction dysplasia syndrome 1

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P
• diencephalic-mesencephalic junction dysplasia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNF14	XM_047417903.1	c.-181+898T>C		intron_variant	Intron 1 of 8		XP_047273859.1
RNF14	XM_047417904.1	c.-181+9913T>C		intron_variant	Intron 1 of 8		XP_047273860.1
RNF14	XM_047417908.1	c.-181+9913T>C		intron_variant	Intron 1 of 7		XP_047273864.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF14	ENST00000511961.5	c.-7+898T>C		intron_variant	Intron 1 of 3	3		ENSP00000423420.1
RNF14	ENST00000506822.5	c.-181+898T>C		intron_variant	Intron 1 of 4	5		ENSP00000423273.1
PCDH12	ENST00000512221.2	n.259-1078A>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.882 AC: 134124 AN: 152058 Hom.: 59446 Cov.: 31

Gnomad AFR AF: 0.959

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.871

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

GnomAD4 genome AF: 0.882 AC: 134236 AN: 152176 Hom.: 59501 Cov.: 31 AF XY: 0.884 AC XY: 65742 AN XY: 74394

African (AFR) AF: 0.959 AC: 39822 AN: 41520

American (AMR) AF: 0.899 AC: 13738 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2778 AN: 3472

East Asian (EAS) AF: 0.991 AC: 5127 AN: 5174

South Asian (SAS) AF: 0.888 AC: 4278 AN: 4816

European-Finnish (FIN) AF: 0.824 AC: 8722 AN: 10590

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57036 AN: 68000

Other (OTH) AF: 0.870 AC: 1839 AN: 2114

Alfa AF: 0.859 Hom.: 31821

Bravo AF: 0.892

Asia WGS AF: 0.913 AC: 3177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.35
DANN	Benign	0.54
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs252109; hg19: chr5-141338888;