rs12404033

chr1-51264382-C-G

Variant summary

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

The NM_014372.5(RNF11):c.124-5574C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 143,558 control chromosomes in the GnomAD database, including 5,999 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 0.26 (5999 hom., cov: 24)
• Consequence: RNF11 NM_014372.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

Genes affected

RNF11 (HGNC:10056): (ring finger protein 11) The protein encoded by this gene contains a RING-H2 finger motif, which is known to be important for protein-protein interactions. The expression of this gene has been shown to be induced by mutant RET proteins (MEN2A/MEN2B). The germline mutations in RET gene are known to be responsible for the development of multiple endocrine neoplasia (MEN). [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNF11	NM_014372.5	c.124-5574C>G		intron_variant		ENST00000242719.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNF11	ENST00000242719.4	c.124-5574C>G		intron_variant		1	NM_014372.5	P1
RNF11	ENST00000494873.1	n.542-6769C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.264 AC: 37869 AN: 143464 Hom.: 5961 Cov.: 24

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.264 AC: 37945 AN: 143558 Hom.: 5999 Cov.: 24 AF XY: 0.260 AC XY: 18034 AN XY: 69246

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.243

Alfa AF: 0.232 Hom.: 592

Bravo AF: 0.274

Asia WGS AF: 0.217 AC: 754 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.012
Dann	Benign	0.52

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: rs12404033; hg19: chr1-51730054;