rs10735098

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001382266.1(RNFT2):​c.883-20909G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 152,054 control chromosomes in the GnomAD database, including 50,934 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 0.81 ( 50934 hom., cov: 31)

Consequence

RNFT2
NM_001382266.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.40
Variant links:
Genes affected
RNFT2 (HGNC:25905): (ring finger protein, transmembrane 2) Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in positive regulation of ERAD pathway and protein ubiquitination. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RNFT2NM_001382266.1 linkuse as main transcriptc.883-20909G>A intron_variant ENST00000257575.9 NP_001369195.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RNFT2ENST00000257575.9 linkuse as main transcriptc.883-20909G>A intron_variant 5 NM_001382266.1 ENSP00000257575.4 Q96EX2-1
RNFT2ENST00000392549.7 linkuse as main transcriptc.883-20909G>A intron_variant 5 ENSP00000376332.2 Q96EX2-1
RNFT2ENST00000407967.7 linkuse as main transcriptc.883-20909G>A intron_variant 5 ENSP00000385669.3 Q96EX2-5
RNFT2ENST00000547718.5 linkuse as main transcriptn.*840-20909G>A intron_variant 2 ENSP00000447294.1 F8VZS7

Frequencies

GnomAD3 genomes
AF:
0.806
AC:
122478
AN:
151936
Hom.:
50926
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.576
Gnomad AMI
AF:
0.863
Gnomad AMR
AF:
0.893
Gnomad ASJ
AF:
0.895
Gnomad EAS
AF:
0.803
Gnomad SAS
AF:
0.757
Gnomad FIN
AF:
0.896
Gnomad MID
AF:
0.867
Gnomad NFE
AF:
0.910
Gnomad OTH
AF:
0.822
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.806
AC:
122525
AN:
152054
Hom.:
50934
Cov.:
31
AF XY:
0.807
AC XY:
60006
AN XY:
74336
show subpopulations
Gnomad4 AFR
AF:
0.576
Gnomad4 AMR
AF:
0.893
Gnomad4 ASJ
AF:
0.895
Gnomad4 EAS
AF:
0.803
Gnomad4 SAS
AF:
0.757
Gnomad4 FIN
AF:
0.896
Gnomad4 NFE
AF:
0.910
Gnomad4 OTH
AF:
0.823
Alfa
AF:
0.890
Hom.:
101705
Bravo
AF:
0.798
Asia WGS
AF:
0.768
AC:
2673
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
8.4
DANN
Benign
0.89

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: rs10735098; hg19: chr12-117250688; API