Genetic Variant RNFT2:c.1201-138C>T (chr12-116849176-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001382266.1(RNFT2):c.1201-138C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 611,004 control chromosomes in the GnomAD database, including 139,447 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 0.55 ( 28828 hom., cov: 30)

Exomes 𝑓: 0.68 ( 110619 hom. )

Consequence

RNFT2
NM_001382266.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.50

Publications

12 publications found

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]

RNFT2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
RNFT2	NM_001382266.1 link	c.1201-138C>T	intron_variant	Intron 10 of 10	ENST00000257575.9	NP_001369195.1
RNFT2	NM_001109903.2 link	c.1201-138C>T	intron_variant	Intron 10 of 11		NP_001103373.1	Q96EX2-1
RNFT2	NM_032814.4 link	c.1201-3474C>T	intron_variant	Intron 10 of 10		NP_116203.2	Q96EX2-5
RNFT2	XM_047429745.1 link	c.1201-3162C>T	intron_variant	Intron 10 of 10		XP_047285701.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNFT2	ENST00000257575.9 link	c.1201-138C>T		intron_variant	Intron 10 of 10	5	NM_001382266.1	ENSP00000257575.4		Q96EX2-1

Frequencies

GnomAD3 genomes

AF:

0.554

AC:

84158

AN:

151816

Hom.:

28819

Cov.:

show subpopulations

Gnomad AFR

AF:

0.138

Gnomad AMI

AF:

0.656

Gnomad AMR

AF:

0.712

Gnomad ASJ

AF:

0.739

Gnomad EAS

AF:

0.450

Gnomad SAS

AF:

0.500

Gnomad FIN

AF:

0.749

Gnomad MID

AF:

0.624

Gnomad NFE

AF:

0.741

Gnomad OTH

AF:

0.593

GnomAD4 exome

AF:

0.678

AC:

311363

AN:

459068

Hom.:

110619

AF XY:

0.672

AC XY:

160982

AN XY:

239564

show subpopulations

African (AFR)

AF:

0.137

AC:

1775

AN:

12958

American (AMR)

AF:

0.768

AC:

15978

AN:

20816

Ashkenazi Jewish (ASJ)

AF:

0.743

AC:

9979

AN:

13432

East Asian (EAS)

AF:

0.443

AC:

13535

AN:

30576

South Asian (SAS)

AF:

0.498

AC:

21513

AN:

43220

European-Finnish (FIN)

AF:

0.762

AC:

22428

AN:

29430

Middle Eastern (MID)

AF:

0.557

AC:

1690

AN:

3034

European-Non Finnish (NFE)

AF:

0.742

AC:

207627

AN:

279862

Other (OTH)

AF:

0.654

AC:

16838

AN:

25740

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

4421

8842

13263

17684

22105

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1436

2872

4308

5744

7180

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.554

AC:

84170

AN:

151936

Hom.:

28828

Cov.:

AF XY:

0.555

AC XY:

41196

AN XY:

74244

show subpopulations

African (AFR)

AF:

0.138

AC:

5712

AN:

41468

American (AMR)

AF:

0.712

AC:

10872

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.739

AC:

2567

AN:

3472

East Asian (EAS)

AF:

0.450

AC:

2319

AN:

5150

South Asian (SAS)

AF:

0.500

AC:

2402

AN:

4800

European-Finnish (FIN)

AF:

0.749

AC:

7898

AN:

10540

Middle Eastern (MID)

AF:

0.629

AC:

185

AN:

294

European-Non Finnish (NFE)

AF:

0.741

AC:

50367

AN:

67930

Other (OTH)

AF:

0.594

AC:

1252

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1363

2726

4090

5453

6816

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

674

1348

2022

2696

3370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.674

Hom.:

102040

Bravo

AF:

0.536

Asia WGS

AF:

0.464

AC:

1617

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.44

(source)

DANN

Benign

0.70

PhyloP100

-1.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over