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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
RNF39	NM_025236.4 link	c.479-16G>A	intron_variant	Intron 3 of 3	ENST00000244360.8	NP_079512.3	Q9H2S5Q96QB5
RNF39	NM_170769.3 link	c.479-16G>A	intron_variant	Intron 3 of 4		NP_739575.3	Q9H2S5A0A1U9X8G2
RNF39	XM_017011325.2 link	c.224-16G>A	intron_variant	Intron 2 of 2		XP_016866814.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF39	ENST00000244360.8 link	c.479-16G>A		intron_variant	Intron 3 of 3	1	NM_025236.4	ENSP00000244360.7		Q9H2S5
RNF39	ENST00000376751.8 link	c.479-16G>A		intron_variant	Intron 3 of 4	1		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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over