11-117246941-G-C

Position:

• chr11-117246941-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_207343.4(RNF214):​c.952G>C​(p.Gly318Arg) variant causes a missense 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. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: RNF214 NM_207343.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.37

Genes affected

RNF214 (HGNC:25335): (ring finger protein 214) Predicted to enable ubiquitin-protein transferase activity. Predicted to be involved in protein ubiquitination. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.16994092).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNF214	NM_207343.4	c.952G>C	p.Gly318Arg	missense_variant	6/15	ENST00000300650.9
RNF214	NM_001077239.2	c.952G>C	p.Gly318Arg	missense_variant	6/15
RNF214	NM_001278249.2	c.487G>C	p.Gly163Arg	missense_variant	6/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNF214	ENST00000300650.9	c.952G>C	p.Gly318Arg	missense_variant	6/15	1	NM_207343.4	P3
RNF214	ENST00000531452.5	c.952G>C	p.Gly318Arg	missense_variant	6/15	1		P3
RNF214	ENST00000531287.5	c.487G>C	p.Gly163Arg	missense_variant	6/15	2		A1
RNF214	ENST00000530849.1	c.487G>C	p.Gly163Arg	missense_variant	5/13	5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.82
BayesDel_addAF	Uncertain	0.019	T
BayesDel_noAF	Benign	-0.21
CADD	Uncertain	26
DANN	Uncertain	1.0
DEOGEN2	Benign	0.027	T;.;T;.
Eigen	Benign	0.18
Eigen_PC	Uncertain	0.22
FATHMM_MKL	Uncertain	0.91	D
LIST_S2	Uncertain	0.94	D;D;.;D
M_CAP	Uncertain	0.089	D
MetaRNN	Benign	0.17	T;T;T;T
MetaSVM	Benign	-0.34	T
MutationAssessor	Benign	0.0	N;.;N;.
MutationTaster	Benign	0.69	D;D;N;N
PrimateAI	Uncertain	0.78	T
PROVEAN	Benign	-1.2	N;N;N;N
REVEL	Benign	0.16
Sift	Uncertain	0.0050	D;D;D;D
Sift4G	Benign	0.30	T;T;T;T
Polyphen		0.96	D;.;D;.
Vest4		0.37
MutPred		0.39		Gain of helix (P = 0.027);.;Gain of helix (P = 0.027);.;
MVP		0.18
MPC		0.30
ClinPred		0.70	D
GERP RS		3.8
RBP_binding_hub_radar		1.1
RBP_regulation_power_radar		2.8
Varity_R		0.12
gMVP		0.47

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-117117657;