dbSNP rs3807032: RNF39:c.-417G>C (chr6-30076002-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
RNF39	NM_025236.4 link	c.-417G>C	upstream_gene_variant	ENST00000244360.8	NP_079512.3	Q9H2S5Q96QB5
RNF39	NM_170769.3 link	c.-417G>C	upstream_gene_variant		NP_739575.3	Q9H2S5A0A1U9X8G2
RNF39	XM_017011325.2 link	c.-649G>C	upstream_gene_variant		XP_016866814.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF39	ENST00000244360.8 link	c.-417G>C		upstream_gene_variant		1	NM_025236.4	ENSP00000244360.7		Q9H2S5
RNF39	ENST00000376751.8 link	c.-417G>C		upstream_gene_variant		1		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

Gnomad4 AFR exome

AF:

0.403

Gnomad4 AMR exome

AF:

0.208

Gnomad4 ASJ exome

AF:

0.166

Gnomad4 EAS exome

AF:

0.171

Gnomad4 SAS exome

AF:

0.152

Gnomad4 FIN exome

AF:

0.0320

Gnomad4 NFE exome

AF:

0.0833

Gnomad4 OTH exome

AF:

0.134

GnomAD4 genome

AF:

0.188

AC:

28587

AN:

152178

Hom.:

4240

Cov.:

AF XY:

0.183

AC XY:

13603

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.404

Gnomad4 AMR

AF:

0.197

Gnomad4 ASJ

AF:

0.172

Gnomad4 EAS

AF:

0.152

Gnomad4 SAS

AF:

0.170

Gnomad4 FIN

AF:

0.0264

Gnomad4 NFE

AF:

0.0854

Gnomad4 OTH

AF:

0.210

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.11

DANN

Benign

0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over