rs1158061

chr13-24793163-C-Gchr13-24793163-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_031277.3(RNF17):c.1057C>G(p.Leu353Val) 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. 14/20 in silico tools predict 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)
• Consequence: RNF17 NM_031277.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243

Genes affected

RNF17 (HGNC:10060): (ring finger protein 17) This gene is similar to a mouse gene that encodes a testis-specific protein containing a RING finger domain. Alternatively spliced transcript variants encoding different isoforms have been found. [provided by RefSeq, May 2010]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.06435606).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNF17	NM_031277.3	c.1057C>G	p.Leu353Val	missense_variant	10/36	ENST00000255324.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNF17	ENST00000255324.10	c.1057C>G	p.Leu353Val	missense_variant	10/36	2	NM_031277.3	P1
RNF17	ENST00000255325.6	c.1057C>G	p.Leu353Val	missense_variant	10/15	2
RNF17	ENST00000255326.4	n.1060C>G		non_coding_transcript_exon_variant	10/12	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.067
BayesDel_addAF	Benign	-0.39	T
BayesDel_noAF	Benign	-0.80
Cadd	Benign	0.49
Dann	Benign	0.32
DEOGEN2	Benign	0.041	T;.
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.072	N
LIST_S2	Benign	0.54	T;T
M_CAP	Benign	0.0042	T
MetaRNN	Benign	0.064	T;T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	1.5	L;L
MutationTaster	Benign	1.0	P;P;P;P
PrimateAI	Benign	0.23	T
PROVEAN	Benign	-0.39	N;.
REVEL	Benign	0.013
Sift	Benign	0.26	T;.
Sift4G	Benign	0.29	T;T
Polyphen		0.024	B;.
Vest4		0.032
MutPred		0.28		Gain of catalytic residue at P358 (P = 5e-04);Gain of catalytic residue at P358 (P = 5e-04);
MVP		0.043
MPC		0.22
ClinPred		0.39	T
GERP RS		1.3
Varity_R		0.037
gMVP		0.12

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1158061; hg19: chr13-25367301;