chr1-51268714-A-G

Position:

• chr1-51268714-A-G

Variant summary

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

The NM_014372.5(RNF11):​c.124-1242A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,286 control chromosomes in the GnomAD database, including 1,265 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 0.11 (1265 hom., cov: 33)
• Consequence: RNF11 NM_014372.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNF11	NM_014372.5	c.124-1242A>G		intron_variant		ENST00000242719.4	NP_055187.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNF11	ENST00000242719.4	c.124-1242A>G		intron_variant		1	NM_014372.5	ENSP00000242719	P1
RNF11	ENST00000494873.1	n.542-2437A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17072 AN: 152168 Hom.: 1268 Cov.: 33

Gnomad AFR AF: 0.0284

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.0956

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.00692

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.112 AC: 17058 AN: 152286 Hom.: 1265 Cov.: 33 AF XY: 0.114 AC XY: 8452 AN XY: 74452

Gnomad4 AFR AF: 0.0283

Gnomad4 AMR AF: 0.0952

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.00693

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.114

Alfa AF: 0.153 Hom.: 1135

Bravo AF: 0.0961

Asia WGS AF: 0.119 AC: 417 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	6.9
DANN	Benign	0.70

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: rs616055; hg19: chr1-51734386;