dbSNP rs2511841: RNF26:p.Thr181Thr (chr11-119335665-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_032015.5(RNF26):c.543G>A(p.Thr181Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 1,613,754 control chromosomes in the GnomAD database, including 389,874 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 0.70 ( 37484 hom., cov: 34)

Exomes 𝑓: 0.69 ( 352390 hom. )

Consequence

RNF26
NM_032015.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.05

Publications

23 publications found

Variant links:

Genes affected

RNF26 (HGNC:14646): (ring finger protein 26) The protein encoded by this intronless gene contains a C3HC5 type of RING finger, a motif known to be involved in protein-DNA and protein-protein interactions. The expression of this gene was found to be upregulated in cancer cell lines derived from different types of cancer. [provided by RefSeq, Jul 2008]

RNF26 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP7

Synonymous conserved (PhyloP=-4.05 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNF26	NM_032015.5 link	c.543G>A	p.Thr181Thr	synonymous_variant	Exon 1 of 1	ENST00000311413.5	NP_114404.1	Q9BY78

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF26	ENST00000311413.5 link	c.543G>A	p.Thr181Thr	synonymous_variant	Exon 1 of 1	6	NM_032015.5	ENSP00000312439.4		Q9BY78

Frequencies

GnomAD3 genomes

AF:

0.701

AC:

106590

AN:

152092

Hom.:

37462

Cov.:

show subpopulations

Gnomad AFR

AF:

0.708

Gnomad AMI

AF:

0.666

Gnomad AMR

AF:

0.754

Gnomad ASJ

AF:

0.614

Gnomad EAS

AF:

0.631

Gnomad SAS

AF:

0.803

Gnomad FIN

AF:

0.709

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.687

Gnomad OTH

AF:

0.679

GnomAD2 exomes

AF:

0.720

AC:

180646

AN:

250934

AF XY:

0.719

show subpopulations

Gnomad AFR exome

AF:

0.714

Gnomad AMR exome

AF:

0.838

Gnomad ASJ exome

AF:

0.596

Gnomad EAS exome

AF:

0.640

Gnomad FIN exome

AF:

0.708

Gnomad NFE exome

AF:

0.689

Gnomad OTH exome

AF:

0.698

GnomAD4 exome

AF:

0.693

AC:

1012873

AN:

1461544

Hom.:

352390

Cov.:

AF XY:

0.696

AC XY:

505748

AN XY:

727032

show subpopulations

African (AFR)

AF:

0.710

AC:

23755

AN:

33480

American (AMR)

AF:

0.827

AC:

36981

AN:

44700

Ashkenazi Jewish (ASJ)

AF:

0.598

AC:

15608

AN:

26098

East Asian (EAS)

AF:

0.666

AC:

26441

AN:

39696

South Asian (SAS)

AF:

0.799

AC:

68944

AN:

86240

European-Finnish (FIN)

AF:

0.714

AC:

38103

AN:

53398

Middle Eastern (MID)

AF:

0.648

AC:

3737

AN:

5768

European-Non Finnish (NFE)

AF:

0.682

AC:

758170

AN:

1111780

Other (OTH)

AF:

0.681

AC:

41134

AN:

60384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

20107

40215

60322

80430

100537

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19494

38988

58482

77976

97470

<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:

0.701

AC:

106656

AN:

152210

Hom.:

37484

Cov.:

AF XY:

0.703

AC XY:

52313

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.707

AC:

29362

AN:

41530

American (AMR)

AF:

0.754

AC:

11537

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.614

AC:

2132

AN:

3470

East Asian (EAS)

AF:

0.631

AC:

3262

AN:

5172

South Asian (SAS)

AF:

0.803

AC:

3874

AN:

4824

European-Finnish (FIN)

AF:

0.709

AC:

7519

AN:

10598

Middle Eastern (MID)

AF:

0.660

AC:

194

AN:

294

European-Non Finnish (NFE)

AF:

0.687

AC:

46737

AN:

68000

Other (OTH)

AF:

0.677

AC:

1432

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1687

3373

5060

6746

8433

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

826

1652

2478

3304

4130

<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:

0.688

Hom.:

162845

Bravo

AF:

0.701

Asia WGS

AF:

0.725

AC:

2517

AN:

3478

EpiCase

AF:

0.674

EpiControl

AF:

0.676

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

0.040

(source)

DANN

Benign

0.85

PhyloP100

-4.1

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