7-5622913-G-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1

The NM_207111.4(RNF216):ā€‹c.2719C>Gā€‹(p.Leu907Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0001 in 1,613,080 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā˜…).

Frequency

Genomes: š‘“ 0.00054 ( 0 hom., cov: 32)
Exomes š‘“: 0.000054 ( 1 hom. )

Consequence

RNF216
NM_207111.4 missense

Scores

4
15

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.90
Variant links:
Genes affected
RNF216 (HGNC:21698): (ring finger protein 216) This gene encodes a cytoplasmic protein which specifically colocalizes and interacts with the serine/threonine protein kinase, receptor-interacting protein (RIP). Zinc finger domains of the encoded protein are required for its interaction with RIP and for inhibition of TNF- and IL1-induced NF-kappa B activation pathways. The encoded protein may also function as an E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes and transfers it to substrates. Several alternatively spliced transcript variants have been described for this locus but the full-length natures of only some are known. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.009888113).
BP6
Variant 7-5622913-G-C is Benign according to our data. Variant chr7-5622913-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 1595954.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000545 (83/152372) while in subpopulation AFR AF= 0.00195 (81/41588). AF 95% confidence interval is 0.0016. There are 0 homozygotes in gnomad4. There are 43 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RNF216NM_207111.4 linkuse as main transcriptc.2719C>G p.Leu907Val missense_variant 17/17 ENST00000389902.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RNF216ENST00000389902.8 linkuse as main transcriptc.2719C>G p.Leu907Val missense_variant 17/171 NM_207111.4 P4Q9NWF9-1
RNF216ENST00000425013.6 linkuse as main transcriptc.2548C>G p.Leu850Val missense_variant 17/171 A1Q9NWF9-2
RNF216ENST00000389900.8 linkuse as main transcriptc.*1836C>G 3_prime_UTR_variant, NMD_transcript_variant 16/161
RNF216ENST00000469375.1 linkuse as main transcript downstream_gene_variant 3

Frequencies

GnomAD3 genomes
AF:
0.000545
AC:
83
AN:
152254
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00195
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000160
AC:
40
AN:
250746
Hom.:
0
AF XY:
0.000111
AC XY:
15
AN XY:
135436
show subpopulations
Gnomad AFR exome
AF:
0.00234
Gnomad AMR exome
AF:
0.0000579
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000541
AC:
79
AN:
1460708
Hom.:
1
Cov.:
31
AF XY:
0.0000440
AC XY:
32
AN XY:
726454
show subpopulations
Gnomad4 AFR exome
AF:
0.00206
Gnomad4 AMR exome
AF:
0.0000671
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000180
Gnomad4 OTH exome
AF:
0.0000828
GnomAD4 genome
AF:
0.000545
AC:
83
AN:
152372
Hom.:
0
Cov.:
32
AF XY:
0.000577
AC XY:
43
AN XY:
74516
show subpopulations
Gnomad4 AFR
AF:
0.00195
Gnomad4 AMR
AF:
0.000131
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000561
Hom.:
0
Bravo
AF:
0.000514
ESP6500AA
AF:
0.00136
AC:
6
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.000123
AC:
15
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.0000545
EpiControl
AF:
0.00

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingInvitaeAug 16, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.091
BayesDel_addAF
Benign
-0.44
T
BayesDel_noAF
Benign
-0.42
CADD
Benign
16
DANN
Uncertain
0.99
DEOGEN2
Benign
0.029
T;.
Eigen
Benign
-0.20
Eigen_PC
Benign
-0.059
FATHMM_MKL
Uncertain
0.89
D
LIST_S2
Benign
0.73
T;T
M_CAP
Benign
0.0078
T
MetaRNN
Benign
0.0099
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.4
L;.
MutationTaster
Benign
0.78
D;D
PrimateAI
Uncertain
0.49
T
PROVEAN
Benign
-0.65
N;N
REVEL
Benign
0.072
Sift
Benign
0.17
T;T
Sift4G
Uncertain
0.028
D;D
Polyphen
0.015
B;B
Vest4
0.36
MVP
0.47
MPC
0.074
ClinPred
0.013
T
GERP RS
4.0
Varity_R
0.030
gMVP
0.21

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

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

Other links and lift over

dbSNP: rs143677963; hg19: chr7-5662544; API