rs10735098

Positions:

• chr12-116812883-G-A
• chr12-116812883-G-C
• chr12-116812883-G-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40

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]

ACMG classification

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
RNFT2	NM_001382266.1	c.883-20909G>A		intron_variant		ENST00000257575.9	NP_001369195.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNFT2	ENST00000257575.9	c.883-20909G>A		intron_variant		5	NM_001382266.1	ENSP00000257575.4
RNFT2	ENST00000392549.7	c.883-20909G>A		intron_variant		5		ENSP00000376332.2
RNFT2	ENST00000407967.7	c.883-20909G>A		intron_variant		5		ENSP00000385669.3
RNFT2	ENST00000547718.5	n.*840-20909G>A		intron_variant		2		ENSP00000447294.1

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122478 AN: 151936 Hom.: 50926 Cov.: 31

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

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

Other links and lift over

dbSNP: rs10735098; hg19: chr12-117250688;