rs9261301

chr6-30073782-G-Achr6-30073782-G-T

Variant summary

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

The NM_025236.4(RNF39):c.364-304C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 151,632 control chromosomes in the GnomAD database, including 21,395 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 0.53 (21395 hom., cov: 30)
• Consequence: RNF39 NM_025236.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNF39	NM_025236.4	c.364-304C>T		intron_variant		ENST00000244360.8
RNF39	NM_170769.3	c.364-304C>T		intron_variant
RNF39	XM_017011325.2	c.132-534C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNF39	ENST00000244360.8	c.364-304C>T		intron_variant		1	NM_025236.4	P1
RNF39	ENST00000376751.8	c.364-304C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80168 AN: 151516 Hom.: 21351 Cov.: 30

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.549

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.529 AC: 80261 AN: 151632 Hom.: 21395 Cov.: 30 AF XY: 0.530 AC XY: 39284 AN XY: 74058

Gnomad4 AFR AF: 0.483

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.553

Alfa AF: 0.541 Hom.: 23529

Bravo AF: 0.532

Asia WGS AF: 0.585 AC: 2035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.0
Dann	Benign	0.73

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: rs9261301; hg19: chr6-30041559;