rs2301751

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_025236.4(RNF39):​c.479-16G>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0489 in 1,397,300 control chromosomes in the GnomAD database, including 1,998 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 0.052 ( 257 hom., cov: 32)
Exomes 𝑓: 0.048 ( 1741 hom. )

Consequence

RNF39
NM_025236.4 splice_polypyrimidine_tract, intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.27
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]

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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=-0.81).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0644 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RNF39NM_025236.4 linkuse as main transcriptc.479-16G>A splice_polypyrimidine_tract_variant, intron_variant ENST00000244360.8
RNF39NM_170769.3 linkuse as main transcriptc.479-16G>A splice_polypyrimidine_tract_variant, intron_variant
RNF39XM_017011325.2 linkuse as main transcriptc.224-16G>A splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RNF39ENST00000244360.8 linkuse as main transcriptc.479-16G>A splice_polypyrimidine_tract_variant, intron_variant 1 NM_025236.4 P1
RNF39ENST00000376751.8 linkuse as main transcriptc.479-16G>A splice_polypyrimidine_tract_variant, intron_variant 1

Frequencies

GnomAD3 genomes
AF:
0.0519
AC:
7902
AN:
152114
Hom.:
256
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0495
Gnomad AMI
AF:
0.0154
Gnomad AMR
AF:
0.0675
Gnomad ASJ
AF:
0.174
Gnomad EAS
AF:
0.0363
Gnomad SAS
AF:
0.0236
Gnomad FIN
AF:
0.0238
Gnomad MID
AF:
0.0475
Gnomad NFE
AF:
0.0516
Gnomad OTH
AF:
0.0598
GnomAD3 exomes
AF:
0.0562
AC:
1086
AN:
19320
Hom.:
40
AF XY:
0.0563
AC XY:
573
AN XY:
10176
show subpopulations
Gnomad AFR exome
AF:
0.0689
Gnomad AMR exome
AF:
0.0603
Gnomad ASJ exome
AF:
0.186
Gnomad EAS exome
AF:
0.0424
Gnomad SAS exome
AF:
0.0316
Gnomad FIN exome
AF:
0.0121
Gnomad NFE exome
AF:
0.0648
Gnomad OTH exome
AF:
0.0716
GnomAD4 exome
AF:
0.0485
AC:
60346
AN:
1245068
Hom.:
1741
Cov.:
30
AF XY:
0.0482
AC XY:
29095
AN XY:
603332
show subpopulations
Gnomad4 AFR exome
AF:
0.0454
Gnomad4 AMR exome
AF:
0.0606
Gnomad4 ASJ exome
AF:
0.165
Gnomad4 EAS exome
AF:
0.0875
Gnomad4 SAS exome
AF:
0.0247
Gnomad4 FIN exome
AF:
0.0253
Gnomad4 NFE exome
AF:
0.0469
Gnomad4 OTH exome
AF:
0.0556
GnomAD4 genome
AF:
0.0520
AC:
7916
AN:
152232
Hom.:
257
Cov.:
32
AF XY:
0.0518
AC XY:
3857
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.0496
Gnomad4 AMR
AF:
0.0678
Gnomad4 ASJ
AF:
0.174
Gnomad4 EAS
AF:
0.0364
Gnomad4 SAS
AF:
0.0237
Gnomad4 FIN
AF:
0.0238
Gnomad4 NFE
AF:
0.0516
Gnomad4 OTH
AF:
0.0587
Alfa
AF:
0.0563
Hom.:
193
Bravo
AF:
0.0545
Asia WGS
AF:
0.0360
AC:
126
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
2.8
DANN
Benign
0.88

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

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

Other links and lift over

dbSNP: rs2301751; hg19: chr6-30039484; API