rs1158061

Variant names:

• chr13-24793163-C-G
• rs1158061
• NM_031277.3:c.1057C>G

Your query was ambiguous. Multiple possible variants found:

• chr13-24793163-C-G
• chr13-24793163-C-T

Variant summary

Our verdict is Likely benign. The variant received -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. 16/22 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
• Publications: 12 publications found

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

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 (MetaRNN=0.06435606).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNF17	NM_031277.3	c.1057C>G	p.Leu353Val	missense_variant	Exon 10 of 36	ENST00000255324.10	NP_112567.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF17	ENST00000255324.10	c.1057C>G	p.Leu353Val	missense_variant	Exon 10 of 36	2	NM_031277.3	ENSP00000255324.5
RNF17	ENST00000255325.6	c.1057C>G	p.Leu353Val	missense_variant	Exon 10 of 15	2		ENSP00000255325.6
RNF17	ENST00000255326.4	n.1060C>G		non_coding_transcript_exon_variant	Exon 10 of 12	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 4507

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
PhyloP100		0.24
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
Mutation Taster		=98/2	polymorphism

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

Other links and lift over

dbSNP: rs1158061; hg19: chr13-25367301;