chr20-49952392-G-C

Variant names:

• chr20-49952392-G-C
• rs6125829
• NM_018683.4:c.*251G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_018683.4(RNF114):​c.*251G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: RNF114 NM_018683.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374
• Publications: 25 publications found

Genes affected

RNF114 (HGNC:13094): (ring finger protein 114) Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in protein polyubiquitination and ubiquitin-dependent protein catabolic process. Located in cytosol and plasma membrane. Biomarker of male infertility. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018683.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF114	NM_018683.4	MANE Select	c.*251G>C		3_prime_UTR	Exon 6 of 6	NP_061153.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF114	ENST00000244061.6	TSL:1 MANE Select	c.*251G>C		3_prime_UTR	Exon 6 of 6	ENSP00000244061.2
	RNF114	ENST00000622999.3	TSL:2	n.*766G>C		non_coding_transcript_exon	Exon 6 of 6	ENSP00000485203.1
	RNF114	ENST00000622920.1	TSL:5	c.*150G>C		3_prime_UTR	Exon 5 of 5	ENSP00000485317.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 387948 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 202578

African (AFR) AF: 0.00 AC: 0 AN: 11650

American (AMR) AF: 0.00 AC: 0 AN: 16908

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12248

East Asian (EAS) AF: 0.00 AC: 0 AN: 29712

South Asian (SAS) AF: 0.00 AC: 0 AN: 32094

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 27546

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1744

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 233128

Other (OTH) AF: 0.00 AC: 0 AN: 22918

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.9
DANN	Benign	0.62
PhyloP100		0.37
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Other links and lift over

dbSNP: rs6125829; hg19: chr20-48568929;