rs9261301

Variant names:

• chr6-30073782-G-A
• rs9261301
• NM_025236.4:c.364-304C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-30073782-G-A
• chr6-30073782-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 24 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 -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 rank	MANE	Protein	UniProt
RNF39	NM_025236.4	c.364-304C>T		intron_variant	Intron 1 of 3	ENST00000244360.8	NP_079512.3
RNF39	NM_170769.3	c.364-304C>T		intron_variant	Intron 1 of 4		NP_739575.3
RNF39	XM_017011325.2	c.132-534C>T		intron_variant	Intron 1 of 2		XP_016866814.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF39	ENST00000244360.8	c.364-304C>T		intron_variant	Intron 1 of 3	1	NM_025236.4	ENSP00000244360.7
RNF39	ENST00000376751.8	c.364-304C>T		intron_variant	Intron 1 of 4	1		ENSP00000365942.4

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

African (AFR) AF: 0.483 AC: 19916 AN: 41270

American (AMR) AF: 0.586 AC: 8936 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2150 AN: 3470

East Asian (EAS) AF: 0.500 AC: 2572 AN: 5142

South Asian (SAS) AF: 0.608 AC: 2921 AN: 4806

European-Finnish (FIN) AF: 0.522 AC: 5470 AN: 10474

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36458 AN: 67916

Other (OTH) AF: 0.553 AC: 1164 AN: 2104

Alfa AF: 0.540 Hom.: 68790

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
PhyloP100		-0.19
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: rs9261301; hg19: chr6-30041559;