rs248232

Variant summary

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

The NM_001410829.1(RNF130):​c.1151-2961A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 152,132 control chromosomes in the GnomAD database, including 27,695 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 0.57 ( 27695 hom., cov: 32)

Consequence

RNF130
NM_001410829.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.442
Variant links:
Genes affected
RNF130 (HGNC:18280): (ring finger protein 130) The protein encoded by this gene contains a RING finger motif and is similar to g1, a Drosophila zinc-finger protein that is expressed in mesoderm and involved in embryonic development. The expression of the mouse counterpart was found to be upregulated in myeloblastic cells following IL3 deprivation, suggesting that this gene may regulate growth factor withdrawal-induced apoptosis of myeloid precursor cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

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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=-0.53).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RNF130NM_001410829.1 linkuse as main transcriptc.1151-2961A>G intron_variant NP_001397758.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RNF130ENST00000522208.6 linkuse as main transcriptc.1151-2961A>G intron_variant 5 ENSP00000429509 A1

Frequencies

GnomAD3 genomes
AF:
0.571
AC:
86810
AN:
152014
Hom.:
27644
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.843
Gnomad AMI
AF:
0.388
Gnomad AMR
AF:
0.645
Gnomad ASJ
AF:
0.529
Gnomad EAS
AF:
0.753
Gnomad SAS
AF:
0.599
Gnomad FIN
AF:
0.450
Gnomad MID
AF:
0.570
Gnomad NFE
AF:
0.397
Gnomad OTH
AF:
0.558
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.571
AC:
86915
AN:
152132
Hom.:
27695
Cov.:
32
AF XY:
0.576
AC XY:
42841
AN XY:
74364
show subpopulations
Gnomad4 AFR
AF:
0.843
Gnomad4 AMR
AF:
0.645
Gnomad4 ASJ
AF:
0.529
Gnomad4 EAS
AF:
0.753
Gnomad4 SAS
AF:
0.597
Gnomad4 FIN
AF:
0.450
Gnomad4 NFE
AF:
0.397
Gnomad4 OTH
AF:
0.561
Alfa
AF:
0.466
Hom.:
9172
Bravo
AF:
0.597
Asia WGS
AF:
0.682
AC:
2372
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.53
CADD
Benign
7.7
DANN
Benign
0.90

Splicing

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: rs248232; hg19: chr5-179350387; API