dbSNP rs3807032: RNF39:c.-417G>C (chr6-30076002-C-G) – 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.-417G>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 603,504 control chromosomes in the GnomAD database, including 8,293 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 0.19 ( 4240 hom., cov: 33)

Exomes 𝑓: 0.11 ( 4053 hom. )

Consequence

RNF39
NM_025236.4 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.65

Publications

10 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:

Genome browser will be placed here

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=-0.78).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.399 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.-417G>C		upstream_gene	N/A	NP_079512.3
	RNF39	NM_170769.3		c.-417G>C		upstream_gene	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.-417G>C		upstream_gene	N/A	ENSP00000244360.7	Q9H2S5
	RNF39	ENST00000376751.8	TSL:1	c.-417G>C		upstream_gene	N/A	ENSP00000365942.4	Q9H2S5

Frequencies

GnomAD3 genomes

AF:

0.188

AC:

28549

AN:

152058

Hom.:

4232

Cov.:

show subpopulations

Gnomad AFR

AF:

0.405

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.197

Gnomad ASJ

AF:

0.172

Gnomad EAS

AF:

0.152

Gnomad SAS

AF:

0.169

Gnomad FIN

AF:

0.0264

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.0854

Gnomad OTH

AF:

0.213

GnomAD4 exome

AF:

0.112

AC:

50682

AN:

451326

Hom.:

4053

AF XY:

0.112

AC XY:

26816

AN XY:

238410

show subpopulations

African (AFR)

AF:

0.403

AC:

4972

AN:

12330

American (AMR)

AF:

0.208

AC:

3786

AN:

18206

Ashkenazi Jewish (ASJ)

AF:

0.166

AC:

2289

AN:

13788

East Asian (EAS)

AF:

0.171

AC:

5253

AN:

30774

South Asian (SAS)

AF:

0.152

AC:

6584

AN:

43380

European-Finnish (FIN)

AF:

0.0320

AC:

944

AN:

29500

Middle Eastern (MID)

AF:

0.193

AC:

424

AN:

2196

European-Non Finnish (NFE)

AF:

0.0833

AC:

22912

AN:

274962

Other (OTH)

AF:

0.134

AC:

3518

AN:

26190

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

2197

4394

6592

8789

10986

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

256

512

768

1024

1280

<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:

0.188

AC:

28587

AN:

152178

Hom.:

4240

Cov.:

AF XY:

0.183

AC XY:

13603

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.404

AC:

16766

AN:

41476

American (AMR)

AF:

0.197

AC:

3009

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.172

AC:

597

AN:

3472

East Asian (EAS)

AF:

0.152

AC:

784

AN:

5160

South Asian (SAS)

AF:

0.170

AC:

821

AN:

4830

European-Finnish (FIN)

AF:

0.0264

AC:

280

AN:

10620

Middle Eastern (MID)

AF:

0.231

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0854

AC:

5807

AN:

67996

Other (OTH)

AF:

0.210

AC:

444

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1063

2127

3190

4254

5317

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

286

572

858

1144

1430

<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:

0.0391

Hom.:

Bravo

AF:

0.216

Asia WGS

AF:

0.161

AC:

560

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.11

(source)

DANN

Benign

0.73

PhyloP100

-2.7

PromoterAI

0.15

Neutral

(source)

Splicing

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