15-59004292-G-T

Variant names:

• chr15-59004292-G-T
• rs1446240
• NM_017610.8:c.-20+16224G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017610.8(RNF111):​c.-20+16224G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 243,988 control chromosomes in the GnomAD database, including 5,970 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 0.22 (4005 hom., cov: 33)
  • Exomes 𝑓: 0.19 (1965 hom.)
• Consequence: RNF111 NM_017610.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• Publications: 6 publications found

Genes affected

RNF111 (HGNC:17384): (ring finger protein 111) The protein encoded by this gene is a nuclear RING-domain containing E3 ubiquitin ligase. This protein interacts with the transforming growth factor (TGF) -beta/NODAL signaling pathway by promoting the ubiquitination and proteosomal degradation of negative regulators, like SMAD proteins, and thereby enhances TGF-beta target-gene transcription. As a modulator of the nodal signaling cascade, this gene plays a critical role in the induction of mesoderm during embryonic development. Alternative splicing of this gene results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017610.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF111	NM_017610.8	MANE Select	c.-20+16224G>T		intron	N/A	NP_060080.6
	RNF111	NM_001330331.2		c.-20+16224G>T		intron	N/A	NP_001317260.1
	RNF111	NM_001270528.2		c.-20+16224G>T		intron	N/A	NP_001257457.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF111	ENST00000348370.9	TSL:1 MANE Select	c.-20+16224G>T		intron	N/A	ENSP00000288199.5
	RNF111	ENST00000559209.5	TSL:1	c.-20+16224G>T		intron	N/A	ENSP00000453872.1
	RNF111	ENST00000557998.5	TSL:2	c.-20+15887G>T		intron	N/A	ENSP00000452732.1

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33106 AN: 151930 Hom.: 3999 Cov.: 33

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.178

GnomAD4 exome AF: 0.188 AC: 17248 AN: 91940 Hom.: 1965 AF XY: 0.197 AC XY: 9437 AN XY: 47798

African (AFR) AF: 0.256 AC: 480 AN: 1874

American (AMR) AF: 0.181 AC: 249 AN: 1372

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 165 AN: 1226

East Asian (EAS) AF: 0.395 AC: 628 AN: 1588

South Asian (SAS) AF: 0.376 AC: 3018 AN: 8026

European-Finnish (FIN) AF: 0.243 AC: 416 AN: 1712

Middle Eastern (MID) AF: 0.153 AC: 73 AN: 478

European-Non Finnish (NFE) AF: 0.160 AC: 11561 AN: 72254

Other (OTH) AF: 0.193 AC: 658 AN: 3410

GnomAD4 genome AF: 0.218 AC: 33135 AN: 152048 Hom.: 4005 Cov.: 33 AF XY: 0.226 AC XY: 16813 AN XY: 74316

African (AFR) AF: 0.273 AC: 11305 AN: 41458

American (AMR) AF: 0.171 AC: 2611 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 580 AN: 3472

East Asian (EAS) AF: 0.408 AC: 2115 AN: 5184

South Asian (SAS) AF: 0.388 AC: 1868 AN: 4818

European-Finnish (FIN) AF: 0.279 AC: 2935 AN: 10530

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11225 AN: 67994

Other (OTH) AF: 0.178 AC: 375 AN: 2108

Alfa AF: 0.189 Hom.: 2464

Bravo AF: 0.208

Asia WGS AF: 0.375 AC: 1300 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.49
PhyloP100		-0.095
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.2
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

Other links and lift over

dbSNP: rs1446240; hg19: chr15-59296491;