chr6-30070870-T-C

Variant names:

• chr6-30070870-T-C
• rs9261290
• NM_025236.4:c.*241A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_025236.4(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 NM_025236.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505
• Publications: 38 publications found

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

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.032).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0998 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF39	NM_025236.4	MANE Select	c.*241A>G		3_prime_UTR	Exon 4 of 4	NP_079512.3
	RNF39	NM_170769.3		c.*241A>G		3_prime_UTR	Exon 5 of 5	NP_739575.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF39	ENST00000244360.8	TSL:1 MANE Select	c.*241A>G		3_prime_UTR	Exon 4 of 4	ENSP00000244360.7
	RNF39	ENST00000376751.8	TSL:1	c.*241A>G		3_prime_UTR	Exon 5 of 5	ENSP00000365942.4

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

GnomAD2 exomes AF: 0.0519 AC: 7253 AN: 139704 AF XY: 0.0517

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 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

African (AFR) AF: 0.0228 AC: 358 AN: 15696

American (AMR) AF: 0.0197 AC: 680 AN: 34494

Ashkenazi Jewish (ASJ) AF: 0.0287 AC: 572 AN: 19926

East Asian (EAS) AF: 0.0000316 AC: 1 AN: 31666

South Asian (SAS) AF: 0.0000646 AC: 4 AN: 61884

European-Finnish (FIN) AF: 0.0577 AC: 1910 AN: 33104

Middle Eastern (MID) AF: 0.00567 AC: 23 AN: 4056

European-Non Finnish (NFE) AF: 0.0980 AC: 30753 AN: 313690

Other (OTH) AF: 0.0636 AC: 1928 AN: 30316

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

African (AFR) AF: 0.0216 AC: 895 AN: 41528

American (AMR) AF: 0.0252 AC: 385 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0265 AC: 92 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4822

European-Finnish (FIN) AF: 0.0532 AC: 564 AN: 10600

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6924 AN: 67994

Other (OTH) AF: 0.0416 AC: 88 AN: 2114

Alfa AF: 0.0884 Hom.: 3242

Bravo AF: 0.0561

Asia WGS AF: 0.00375 AC: 14 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.20
PhyloP100		-0.51
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9261290; hg19: chr6-30038647;