17-58355015-G-A

Variant names:

• chr17-58355015-G-A
• rs2158459
• NM_017763.6:c.2309-29C>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_017763.6(RNF43):​c.2309-29C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00372 in 1,604,970 control chromosomes in the GnomAD database, including 165 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.020 (86 hom., cov: 32)
  • Exomes 𝑓: 0.0020 (79 hom.)
• Consequence: RNF43 NM_017763.6 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -0.0890

Genes affected

RNF43 (HGNC:18505): (ring finger protein 43) The protein encoded by this gene is a RING-type E3 ubiquitin ligase and is predicted to contain a transmembrane domain, a protease-associated domain, an ectodomain, and a cytoplasmic RING domain. This protein is thought to negatively regulate Wnt signaling, and expression of this gene results in an increase in ubiquitination of frizzled receptors, an alteration in their subcellular distribution, resulting in reduced surface levels of these receptors. Mutations in this gene have been reported in multiple tumor cells, including colorectal and endometrial cancers. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2015]

ENSG00000285897 (HGNC:):

TSPOAP1-AS1 (HGNC:44148): (TSPOAP1, SUPT4H1 and RNF43 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 17-58355015-G-A is Benign according to our data. Variant chr17-58355015-G-A is described in ClinVar as [Benign]. Clinvar id is 1235832.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNF43	NM_017763.6	c.2309-29C>T		intron_variant	Intron 9 of 9	ENST00000407977.7	NP_060233.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF43	ENST00000407977.7	c.2309-29C>T		intron_variant	Intron 9 of 9	2	NM_017763.6	ENSP00000385328.2
ENSG00000285897	ENST00000648873.1	n.2308+2453C>T		intron_variant	Intron 8 of 12			ENSP00000497686.1

Frequencies

GnomAD3 genomes AF: 0.0199 AC: 3034 AN: 152196 Hom.: 85 Cov.: 32

Gnomad AFR AF: 0.0681

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0107

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000279

Gnomad OTH AF: 0.0129

GnomAD2 exomes AF: 0.00512 AC: 1275 AN: 248930 AF XY: 0.00391

Gnomad AFR exome AF: 0.0684

Gnomad AMR exome AF: 0.00348

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000259

Gnomad OTH exome AF: 0.00343

GnomAD4 exome AF: 0.00202 AC: 2929 AN: 1452656 Hom.: 79 Cov.: 28 AF XY: 0.00175 AC XY: 1267 AN XY: 723224

Gnomad4 AFR exome AF: 0.0681 AC: 2258 AN: 33176

Gnomad4 AMR exome AF: 0.00426 AC: 190 AN: 44646

Gnomad4 ASJ exome AF: 0.0000384 AC: 1 AN: 26066

Gnomad4 EAS exome AF: 0.00 AC: 0 AN: 39654

Gnomad4 SAS exome AF: 0.000221 AC: 19 AN: 85916

Gnomad4 FIN exome AF: 0.00 AC: 0 AN: 53342

Gnomad4 NFE exome AF: 0.000132 AC: 146 AN: 1104402

Gnomad4 Remaining exome AF: 0.00479 AC: 288 AN: 60068

GnomAD4 genome AF: 0.0200 AC: 3045 AN: 152314 Hom.: 86 Cov.: 32 AF XY: 0.0191 AC XY: 1424 AN XY: 74480

Gnomad4 AFR AF: 0.0682 AC: 0.0681938 AN: 0.0681938

Gnomad4 AMR AF: 0.0107 AC: 0.0107176 AN: 0.0107176

Gnomad4 ASJ AF: 0.000288 AC: 0.000288018 AN: 0.000288018

Gnomad4 EAS AF: 0.00 AC: 0 AN: 0

Gnomad4 SAS AF: 0.000207 AC: 0.000207211 AN: 0.000207211

Gnomad4 FIN AF: 0.00 AC: 0 AN: 0

Gnomad4 NFE AF: 0.000265 AC: 0.000264581 AN: 0.000264581

Gnomad4 OTH AF: 0.0128 AC: 0.0127841 AN: 0.0127841

Alfa AF: 0.0107 Hom.: 13

Bravo AF: 0.0233

Asia WGS AF: 0.00404 AC: 14 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Jun 27, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

not specified Benign:1

Mar 04, 2025

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.8
DANN	Benign	0.70
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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: rs2158459; hg19: chr17-56432376;