rs11939380

Positions:

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000433731.7(RNF212):​c.247-2245A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.58 ( 27038 hom., cov: 32)
Failed GnomAD Quality Control

Consequence

RNF212
ENST00000433731.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.33
Variant links:
Genes affected
RNF212 (HGNC:27729): (ring finger protein 212) This gene encodes a RING finger protein that may function as a ubiquitin ligase. The encoded protein may be involved in meiotic recombination. This gene is located within a linkage disequilibrium block and polymorphisms in this gene may influence recombination rates. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Oct 2010]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RNF212NM_001131034.4 linkuse as main transcriptc.247-2245A>G intron_variant ENST00000433731.7 NP_001124506.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RNF212ENST00000433731.7 linkuse as main transcriptc.247-2245A>G intron_variant 1 NM_001131034.4 ENSP00000389709 A2Q495C1-1

Frequencies

GnomAD3 genomes
AF:
0.578
AC:
87716
AN:
151720
Hom.:
27043
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.352
Gnomad AMI
AF:
0.479
Gnomad AMR
AF:
0.565
Gnomad ASJ
AF:
0.720
Gnomad EAS
AF:
0.618
Gnomad SAS
AF:
0.688
Gnomad FIN
AF:
0.677
Gnomad MID
AF:
0.668
Gnomad NFE
AF:
0.685
Gnomad OTH
AF:
0.607
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.578
AC:
87736
AN:
151838
Hom.:
27038
Cov.:
32
AF XY:
0.579
AC XY:
42966
AN XY:
74182
show subpopulations
Gnomad4 AFR
AF:
0.352
Gnomad4 AMR
AF:
0.564
Gnomad4 ASJ
AF:
0.720
Gnomad4 EAS
AF:
0.617
Gnomad4 SAS
AF:
0.688
Gnomad4 FIN
AF:
0.677
Gnomad4 NFE
AF:
0.685
Gnomad4 OTH
AF:
0.608
Alfa
AF:
0.595
Hom.:
6629
Bravo
AF:
0.556
Asia WGS
AF:
0.605
AC:
2102
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
6.3
DANN
Benign
0.78

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11939380; hg19: chr4-1086871; API