rs9511479

Positions:

• chr13-24858077-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031277.3(RNF17):​c.3611-924C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 151,942 control chromosomes in the GnomAD database, including 4,531 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 0.23 (4531 hom., cov: 32)
• Consequence: RNF17 NM_031277.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNF17	NM_031277.3	c.3611-924C>T		intron_variant		ENST00000255324.10	NP_112567.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNF17	ENST00000255324.10	c.3611-924C>T		intron_variant		2	NM_031277.3	ENSP00000255324.5
RNF17	ENST00000418120.5	c.1583-924C>T		intron_variant		5		ENSP00000388892.1
RNF17	ENST00000339524.3	c.767-924C>T		intron_variant		2		ENSP00000344776.3

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35102 AN: 151824 Hom.: 4537 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.231 AC: 35080 AN: 151942 Hom.: 4531 Cov.: 32 AF XY: 0.229 AC XY: 17035 AN XY: 74240

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.229

Alfa AF: 0.266 Hom.: 985

Bravo AF: 0.222

Asia WGS AF: 0.231 AC: 805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.49
DANN	Benign	0.42

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

LitVar

Other links and lift over

dbSNP: rs9511479; hg19: chr13-25432215;