rs9261290

Positions:

• chr6-30070870-T-C
• chr6-30070870-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000244360.8(RNF39):​c.*241A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.065 in 697,058 control chromosomes in the GnomAD database, including 2,416 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 0.060 (432 hom., cov: 33)
  • Exomes 𝑓: 0.066 (1984 hom.)
• Consequence: RNF39 ENST00000244360.8 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0998 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNF39	NM_025236.4	c.*241A>G		3_prime_UTR_variant	4/4	ENST00000244360.8	NP_079512.3
RNF39	NM_170769.3	c.*241A>G		3_prime_UTR_variant	5/5		NP_739575.3
RNF39	XM_017011325.2	c.*241A>G		3_prime_UTR_variant	3/3		XP_016866814.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNF39	ENST00000244360.8	c.*241A>G		3_prime_UTR_variant	4/4	1	NM_025236.4	ENSP00000244360	P1
RNF39	ENST00000376751.8	c.*241A>G		3_prime_UTR_variant	5/5	1		ENSP00000365942

Frequencies

GnomAD3 genomes AF: 0.0598 AC: 9090 AN: 152110 Hom.: 432 Cov.: 33

Gnomad AFR AF: 0.0216

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0253

Gnomad ASJ AF: 0.0265

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.0532

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0421

GnomAD3 exomes AF: 0.0519 AC: 7253 AN: 139704 Hom.: 376 AF XY: 0.0517 AC XY: 3917 AN XY: 75728

Gnomad AFR exome AF: 0.0220

Gnomad AMR exome AF: 0.0192

Gnomad ASJ exome AF: 0.0291

Gnomad EAS exome AF: 0.0000951

Gnomad SAS exome AF: 0.0000889

Gnomad FIN exome AF: 0.0572

Gnomad NFE exome AF: 0.102

Gnomad OTH exome AF: 0.0551

GnomAD4 exome AF: 0.0665 AC: 36229 AN: 544832 Hom.: 1984 Cov.: 2 AF XY: 0.0637 AC XY: 18795 AN XY: 295078

Gnomad4 AFR exome AF: 0.0228

Gnomad4 AMR exome AF: 0.0197

Gnomad4 ASJ exome AF: 0.0287

Gnomad4 EAS exome AF: 0.0000316

Gnomad4 SAS exome AF: 0.0000646

Gnomad4 FIN exome AF: 0.0577

Gnomad4 NFE exome AF: 0.0980

Gnomad4 OTH exome AF: 0.0636

GnomAD4 genome AF: 0.0597 AC: 9089 AN: 152226 Hom.: 432 Cov.: 33 AF XY: 0.0541 AC XY: 4025 AN XY: 74452

Gnomad4 AFR AF: 0.0216

Gnomad4 AMR AF: 0.0252

Gnomad4 ASJ AF: 0.0265

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.0532

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.0416

Alfa AF: 0.0868 Hom.: 1322

Bravo AF: 0.0561

Asia WGS AF: 0.00375 AC: 14 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.20

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

LitVar

Other links and lift over

dbSNP: rs9261290; hg19: chr6-30038647;