Genetic Variant RNF39:c.479-16G>A (chr6-30071707-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_025236.4(RNF39):c.479-16G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0489 in 1,397,300 control chromosomes in the GnomAD database, including 1,998 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 0.052 ( 257 hom., cov: 32)

Exomes 𝑓: 0.048 ( 1741 hom. )

Consequence

RNF39
NM_025236.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.27

Publications

18 publications found

Variant links:

Genes affected

RNF39 (HGNC:18064): (ring finger protein 39) This gene lies within the major histocompatibility complex class I region on chromosome 6. Studies of a similar rat protein suggest that this gene encodes a protein that plays a role in an early phase of synaptic plasticity. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

RNF39 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=-0.81).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0644 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025236.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF39	NM_025236.4	MANE Select	c.479-16G>A		intron	N/A	NP_079512.3
	RNF39	NM_170769.3		c.479-16G>A		intron	N/A	NP_739575.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF39	ENST00000244360.8	TSL:1 MANE Select	c.479-16G>A		intron	N/A	ENSP00000244360.7	Q9H2S5
	RNF39	ENST00000376751.8	TSL:1	c.479-16G>A		intron	N/A	ENSP00000365942.4	Q9H2S5

Frequencies

GnomAD3 genomes

AF:

0.0519

AC:

7902

AN:

152114

Hom.:

256

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0495

Gnomad AMI

AF:

0.0154

Gnomad AMR

AF:

0.0675

Gnomad ASJ

AF:

0.174

Gnomad EAS

AF:

0.0363

Gnomad SAS

AF:

0.0236

Gnomad FIN

AF:

0.0238

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0516

Gnomad OTH

AF:

0.0598

GnomAD2 exomes

AF:

0.0562

AC:

1086

AN:

19320

AF XY:

0.0563

show subpopulations

Gnomad AFR exome

AF:

0.0689

Gnomad AMR exome

AF:

0.0603

Gnomad ASJ exome

AF:

0.186

Gnomad EAS exome

AF:

0.0424

Gnomad FIN exome

AF:

0.0121

Gnomad NFE exome

AF:

0.0648

Gnomad OTH exome

AF:

0.0716

GnomAD4 exome

AF:

0.0485

AC:

60346

AN:

1245068

Hom.:

1741

Cov.:

AF XY:

0.0482

AC XY:

29095

AN XY:

603332

show subpopulations

African (AFR)

AF:

0.0454

AC:

1115

AN:

24566

American (AMR)

AF:

0.0606

AC:

967

AN:

15946

Ashkenazi Jewish (ASJ)

AF:

0.165

AC:

2914

AN:

17680

East Asian (EAS)

AF:

0.0875

AC:

2550

AN:

29132

South Asian (SAS)

AF:

0.0247

AC:

1478

AN:

59738

European-Finnish (FIN)

AF:

0.0253

AC:

749

AN:

29592

Middle Eastern (MID)

AF:

0.0492

AC:

187

AN:

3802

European-Non Finnish (NFE)

AF:

0.0469

AC:

47522

AN:

1013076

Other (OTH)

AF:

0.0556

AC:

2864

AN:

51536

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

3053

6105

9158

12210

15263

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1856

3712

5568

7424

9280

<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:

0.0520

AC:

7916

AN:

152232

Hom.:

257

Cov.:

AF XY:

0.0518

AC XY:

3857

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.0496

AC:

2059

AN:

41536

American (AMR)

AF:

0.0678

AC:

1038

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.174

AC:

605

AN:

3470

East Asian (EAS)

AF:

0.0364

AC:

188

AN:

5166

South Asian (SAS)

AF:

0.0237

AC:

114

AN:

4820

European-Finnish (FIN)

AF:

0.0238

AC:

252

AN:

10610

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0516

AC:

3507

AN:

68006

Other (OTH)

AF:

0.0587

AC:

124

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

371

742

1114

1485

1856

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

246

328

410

<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:

0.0559

Hom.:

734

Bravo

AF:

0.0545

Asia WGS

AF:

0.0360

AC:

126

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

2.8

(source)

DANN

Benign

0.88

PhyloP100

-1.3

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over